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First of all: Beika of course isn't real. :p But Gosho Aoyama once said it's a combination of real and fictional parts mixed up and the Manga indeed is ripe with little hints to where it would approximately be located if it would exist. The town of Beika and its equally fictional neighbouring districts like Haido, Toriya, Buraku and Sutan are set in a fictionalized ward of Tokyo (Beika Ward (米花区 ,Beika-ku^?)) which is roughly located on/in a real-life area consisting of a good chunk of northern Minato (maybe a third or even half of it), as well as small parts of Chiyoda, Shibuya and Shinagawa (and maybe a little of the south of Shinjuku) bordering on it - or on a made-up piece of land between all of those. This position of Beika is pretty consistent throughout the Manga and suggested by the following evidence.

Professor Agasa's full address is revealed to be City of Tokyo, Beika Ward, Beika Town, 2nd Block, street address 22 (東京都米花区米花町２丁目２２番地 ,Tōkyō-to Beika-ku Beika-chō 2-chōme 22-banchi^?) in FILE.843, proving that Beika is a district in a fictional ward of the same name in Tokyo.

In FILE.14 (Volume 2, File 5), Conan Edogawa is on the way back from the Beika Police Department to the Mouri Detective Agency together with Kogoro and Ran Mouri, during which he - with the help of his new glasses gadget - geolocates the tall man "4 kilometers to the northwest... in Shinjuku", which, if you take any point in Shinjuku, would encompass exactly the area tinted and framed in blue on the following map for Conan (and the part of Beika seen here) to potentially be in - consisting of a good chunk of the upper half of Minato, the lower half of Chiyoda and a remote southeast corner of Shinjuku itself.

Conan came from somewhere in the area tinted and framed in blue.

The Detective Boys take a bus on the (back then) real To06 line (都06) of Toei Bus in FILE.37 (Volume 4, File 10) to get from Beika (or, rather, a bus stop close to Beika Park, it seems) to the Tokyo Tower. The line indeed lead from Shibuya Station through Minato Ward, stopped at the Tower and had its final destination at Shimbashi Station. The complete route can be seen as a green line on the following map.

The green line, symbolizing the To06 bus route, would lead through Beika.

Conan meets Kaitou Kid for the first time in FILE.156 on the roof of the Haido City Hotel. The view from it over a portion of the Minato Ward, including Tokyo Tower and the Shiroyama Trust Tower to the left of it, firmly places the fictional building on the position of the real ANA Intercontinental Tokyo Hotel, even though the buildings look differently.

Kid and Conan with the panorama of Minato behind them - including the Shiroyama Trust and Tokyo Tower.

Shortly before that, Conan takes a look around, to the right of Tokyo Tower, and watches a bunch of searchlights scouring the sky, commenting that this is where Beika Museum should be - which would place it approximately where the Azabu Districts (including Roppongi) are in real life.

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Conan watching the searchlights over Beika Museum - which would be somewhere around Azabu in real life.

In FILE.267 - 269, a serial arsonist sets fire to several places in Tokyo, the last of which so far is in Yotsuya, a district in Shinjuku, where Ayumi Yoshida saw the arsonist after he started the fire. Shortly after being interrogated by inspector Miwako Sato at the Tokyo Metropolitan Police Department about the person in question, she wants to drive to Yotsuya together with the Detective Boys, saying that she wants to take a stop anyway, since it's "the same way" - which is revealed to be the 4th block of Haido, where her father happened to die 18 years ago, firmly placing this block of the fictitious district somewhere between the real districts of Kasumigaseki (Chiyoda Ward) and the aforementioned Yotsuya - in an area on the southwest border of Chiyoda it shares with Minato Ward.

On the route between the Tokyo Metropolitan Police Department and Yotsuya, inspector Shiratori tells Megure that Takagi, Satō and himself are at the 4th block of Haido.

To be continued...

Anime

Models

Model	Anime	Description
		Tōto Tower in Episode 4: The Coded Map of the City Case (Season 1, Episode 4) of course is Tokyo Tower in anything but name. It goes on to become a recurring location, implied to be very close to Beika and Haido, maybe even part of it in the world of Detective Conan.
		The kidnapper in Episode 65: A Crab and Whale Kidnapping Case (Season 3, Episode 11) demands the money to be handed over at Karajuku Station (空宿駅 Karajuku-eki), which is a fictionalized version of Harajuku Station (原宿駅 Harajuku-eki), in real life located in the Jingumae District of Shibuya Ward in Tokyo.
		Kurisuke Agasa's mansion in Episode 163-164: The Secret of the Moon, the Star, and the Sun (Season 7, Episode 1-2) is modeled after the "Ohana Estate" mansion in Yanagawa City, located in the Fukuoka Prefecture.
		The place Professor Agasa, Conan Edogawa, Ai Haibara and the Detective Boys drive to in Episode 765 - 766: Teimuzu River Kite Flying Case (Season 24, Episode 26 - 27) is the Horikirimizube Park at the first block of the Horikiri District in the Katsushika Ward of Tokyo, with the Arakawa doubling as Teimuzu River in Detective Conan. The aforementioned park indeed is a popular spot for kite flying competitions in real life. The bridge sporting these distinct Y-shaped concrete pylons seen several times next to the park in the same case, on the other hand, is the Shin-Arakawa Bridge.
		The cinema Kogoro Mouri and Eri Kisaki go to at the end of Episode 902: Lawyer Kisaki's SOS (Season 28, Episode 5) is modeled after the Cinemas Q in Naha, Okinawa Prefecture, in real life on the island of Kyushu.
		The kendō tournament Heiji Hattori, Soshi Okita and Takeshi Onimaru partake in during Episode 916-917: The Kendo Tournament of Love and Mystery (Season 28, Episodes 19-20) is organized in Tōto Gymnasium, which is based on the real Nakano Gymnasium, located at 4-11-14 Nakano District_(jp) in the ward of the same name, Tokyo.
		The "Danny's" Amuro, Conan and the Detective Boys are stopping by to eat and discuss their hunt for the phone strap in Episode 925: The Heartfelt Strap (Season 28, Episode 28 - 29) is a real Denny's restaurant - the one at 1-chōme 6−1 in Yokohama's Kitayamada District in the Tsuzuki Ward (Kanagawa Prefecture), to be specific. Considering Amuro must have passed Yokohama to reach Chiyari Station, it's a fitting location to stop.

Detective Conan: Wild Police Story

Models

Model	Manga	Description
		The Metropolitan Police Academy Tokyo from Rei's Manga spin-off is just that: The real Metropolitan Police Academy. It's called by its actual name and also looks the same in the Manga. No renaming or anything. It's not actually in the City of Tokyo, but part of it's Metropolitan Area - in the City of Fuchū. This is also mentioned in the Wikipedia article.

Magic Kaito

Manga

Models

Model	Manga	Description
		Ekoda High School - in this incarnation from Chapter 1 (Magic Kaito Volume 1, Chapter 1) onwards - is very probably based on the main building (#3) on the Ekoda Campus of Musashi University, right next to the Ekoda Campus (fine arts) of Nihon University, where Gosho Aoyama and Yutaka Abe (a past mentor and current assistant of his) studied and lived - also not far away from Ekoda Station, which was close to Gosho's apartment. Interestingly enough, building #3 was a high school once and what is the Ekoda Campus of Nihon today once housed another high school associated with the university, called Ekoda High School (also shortened as 江古田高校 ([i]Ekoda kōkō[/i]), like the school in the Manga), which closed in 1976 and is also used as a university building today. All of the mentioned campuses and buildings are located in the adjacent neighbourhoods of Asahigaoka and Toyotamakami in Nerima Ward. Ekoda High School was first used by Yutaka Abe in 100% Tantei Monogatari in 1986 (set in the same universe as Magic Kaito and made with the assistance of Gosho).
		The crossroads the helicopters pass close to the end of the first chapter to catch Kaitou Kid is a real crossing in the fourth block of Ginza (Chūō Ward, Tokyo), especially identifiable by the Fujiya store to the left. The view would thus be to the southeast, with the helicopters in consequence flying to the northeast to reach "Ono Bank" (which probably was a nod to the Tokyo Bank, which indeed was located in Nihonbashi - to the northeast of Ginza - back then (before merging with Mitsubishi Bank and moving to Chiyoda Ward), which is supported by the fact that "Ono" was a generic placeholder word for terms with "Tokyo" and "Japan" in it, used by Gosho in the same vein as "Tohto" nowadays). Interestingly, this intersection is right next to another famous crossroads in Ginza - the one Kid did his midair walk over in Detective Conan later on.
		During Kaito's and Konosuke Jii's fateful encounter, still in the first chapter, a night-time view of Hotel New Otani Tokyo and its surroundings in the Kioi District of Chiyoda Ward (Tokyo) can be seen.
		Kaito Kuroba's route from school leads him along a river, which, based on the surroundings, looks a lot like the Arakawa or Edo River and one of their Warren truss steel railway bridges, like this one, this one or this one, for example. In Chapter 2 (Magic Kaito Volume 1, Chapter 2), he meets the depressed inspector Ginzo Nakamori sitting at the riverbank and cheers him up and in Chapter 19 (Magic Kaito Volume 3, Chapter 6) he passes the same spot again. Gosho lived in the Adachi Ward of Tokyo for a while^[1], through which the Arakawa flows and several of these bridges exist - so it maybe served as the inspiration for these moments.
		Kaito Kuroba and Aoko Nakamori leave one of the central gates of Ikebukuro Station (Ikebukuro District in the Toshima Ward of Tokyo) on their way from school in Chapter 8 (Magic Kaito Volume 2, Chapter 2). The train station is also named as such.
		A good chunk of Chapter 11 (Magic Kaito Volume 2, Chapter 5) revolves around a fake accouncement of Kaitou Kid appearing in Tokyo Dome - which he does, in the end. Tokyo Dome is depicted like it is in real life, situated in the Bunkyō Ward. Moreover, according to Gosho himself, he and his editor were especially thrilled by the scenario of Kid appearing on a pole in Tokyo Dome for a story.^[2]
		The distinctive tower of the Ekoda Museum is actually based on one of three popular towers in Yokohama's Naka Ward, the clock tower of the Honcho Building, also known as "Jack's Tower", or just "The Jack".
		The new morning after the night of Kaitou Kid's and Yaiba Kurogane's battle in Chapter 18 (Magic Kaito Volume 3, Chapter 5) is symbolized by a caricature version of Mount Fuji, which is a real volcano on the boundary between the Prefectures of Shizuoka and Yamanashi and within sight of Tokyo.
		Saguru Hakuba is staying in a hotel in Paris in Chapter 25 (Magic Kaito Volume 4, Chapter 5), with the Eiffel Tower clearly visible in the background.
		The Tokyo Metropolitan Police Department (also known as Keishichō) appearing from Chapter 27 (Magic Kaito Volume 4, Chapter 7) onwards is the real thing from the Kasumigaseki District of Chiyoda Ward, just like it is in Detective Conan. It's real life address is also given in Chapter 29 (Magic Kaito Volume 5, Chapter 1).
		The unnamed museum from the very beginning of the first chapter of "Midnight Crow" (Chapter 31 / Magic Kaito Volume 5, Chapter 3) and the whole of "Sun Halo" (Chapters 34 - 36 / Magic Kaito Volume 5, Chapter 6 - 8) is modeled after the National Museum of Nature and Science in the northeast of Ueno Park in the district of the same name - Ueno in Taitō Ward of Tokyo.
		Harry Nezu arrives in Tokyo and gets interviewed at the Haneda Airport in Chapter 31 (Magic Kaito Volume 5, Chapter 3), which is in the Ōta Ward.
		The skyscraper from Chapter 31 - 33 (Magic Kaito Volume 5, Chapter 3 - 5) in Tokyo where Kaitou Kid and Kaitou Corbeau have their duel with the organization in is modeled after the look of the Yokkaichi Portbuilding (四日市港ポートビル) in the City of Yokkaichi, in real life located in the Mie Prefecture.
		The Sandei Temple is modeled after the Nageire Temple in Gosho's home prefecture Tottori, as was also confirmed by him in his comments accompanying these chapters and the in-story explanation that it is said that the Sandei was directly built after the image of the Nageire (which is denied by the priestess Niwano Yasuyo).

Magic Kaito: Kid the Phantom Thief Anime Specials

Models

Model	Anime	Description
		AITAvision, which appears in several episodes, is ALTAvision (on Studio ALTA) in reality, located in the south of Shinjuku Ward, in the third block of the district of the same name, with the Mitsubishi logo changed to "Mitsubashi".
		The cable-stayed bridge partly visible on Kaito Kuroba's and Aoko Nakamori's way home seems to be modeled after the Tsubaki Sakura Bridge (辰巳桜橋), actually located in the Kōtō Ward of Tokyo and connecting the districts of Tatsumi and Shinonome across Tatsumi River.
		The airport Princess Anne of Sublina arrives at in Episode 3: The Princess Prefers Magic is the Narita International Airport, situated on the border between the towns of Narita and Shibayama in the Chiba Prefecture, which is part of the Greater Tokyo Area.
		One shot in Episode 4: A Witch Sheds No Tears from across the river to the Tokyo Sky Tree is a real spot on a promenade at the Sumida River in the Asakusa District in the Taitō Ward, right next to the Tobu Line Sumida River Bridge visible to the left. This shot also exemplifies that the skyscraper Kaitou Kid used to skate to the Sky Tree, neighboring it, is completely fictional.
		Minato Arena in Episode 7: The Splendid Rivals, in which Gunter von Goldberg II organizes his illusion show in, is modeled after the Yokohama Arena in the third block of the Shin-Yokohama District in the Kohoku Ward of Yokohama.
		The distinct tower of the Ekoda Museum in that same episode, on the other hand, is based on the "Jack's Tower" in the Naka Ward of Yokohama again - just like it was in the manga (see above).

Magic Kaito 1412 Anime

Models

Model	Anime	Description
		This incarnation of Ekoda High School is modeled after the Tokyo Metropolitan High School of Fine Arts, Performing Arts and Classical Music (Tōkyō-to Sōgō Geijutsu Kōtō Gakkō) and its immediate surroundings, located in the Tomihisa District of the Shinjuku Ward of Tokyo.
		The police station inspector Ginzo Nakamori works at is directly modeled after the Tachikawa Police Station in the City of Tachikawa, Greater Tokyo Area.
		Akako Koizumi's mansion in Episode 5: A Temptation in Scarlet and Episode 8: The Adult's Charm is roughly modeled after the Bansui-sō, a real mansion in the Ehime Prefecture on Shikoku.
		The place she confronts Kaitou Kid on during her time stop in Episode 5 also is a real (and famous) crossing in the Ward of Shibuya, especially identifiable by the Tsutaya Building (which was renamed "Sutaya" in the episode) to the right.
		The incarnation of Tropical Land featured in Episode 7: Kaito Kuroba's Busy Holiday pretty much is Tokyo Disneyland in anything but name. The entrance gates and surrounding areas are almost identical...
		... and the Mysterious House is a dead ringer für the Haunted Mansion. The Tropical Land also features a castle extremely similar in architecture to the Cinderella Castle, both situated in the center of its respective parks.
		The skyscraper Kaitou Kid breaks into and tries to escape to Tokyo Tower from in Episode 8: The Adult's Charm actually is the Sompo Japan Nipponkoa Head Office Building, normally located in the skyscraper district Nishi-Shinjuku of Shinjuku Ward and not right next to the Tokyo Tower, as depicted here.
		Kaitou Kid returns Ryōma's Three Treasures in Episode 10: The Phantom Lady and Ryoma's Treasure to a museum which is clearly based on the Tokyo National Museum Hyokeikan and its distinct bronze lions next to the entrance, who also serve as its mascot(s). In reality, it's located in Ueno Park in the district of the same name, located in the Taitō Ward of Tokyo.
		The ski resort the Ekoda High School classes drive to in Episode 13: Stay Away From Him is inspired by the Hakuba Cortina Snow Resort (no relation to the character of the same name) in the village of Hakuba in the aptly named "Hakuba Valley" in Nagano Prefecture.
		The cinema Kaito and Aoko want to visit in Episode 22: Red Tear is a real cinema in the Shinjuku Picadilly Complex in the district and the ward of the same name.
		Before we see Kaitou Kid at "work" inside the museum at the beginning of Episode 23: Midnight Crow (Part 1: The Name is Phantom Thief Corbeau!), we get a shot of the Yasukuni Drive in Shinjuku, including the SHIDAX Building (renamed "SHIDIX" here). The museum in this Anime seems to replace the real building right next to (the left of) SHIDAX.
		Early in that same episode, Harry Nezu arrives in Tokyo at Haneda Airport, which is in the Ōta Ward.
		The skyscraper from Episode 23 - 24 in Tokyo where Kaitou Kid and Kaitou Corbeau have their duel with the organization in is - just like it was in the Manga - modeled after the look of the Yokkaichi Portbuilding (四日市港ポートビル) in the City of Yokkaichi, in real life located in the Mie Prefecture.

Yaiba

Manga

Models

Model	Manga	Description
		The unnamed jungle Yaiba Kurogane and his father live in seems to be (intentionally) highly ambigious about what jungle or even where it could remotely be. Besides the rather generous surroundings, animals like Gorillas (from Sub-Saharan Africa), Tigers (having their habitat in continental Asia) and Jaguars (who usually live in Central and South America) seem to have their habitat there.
		The airport Yaiba Kurogane, his father Kenjuro and their tiger Kategora arrive at in Chapter 1 (Yaiba Volume 1, Chapter 1) is the real Narita International Airport on the border between the towns of Narita and Shibayama in the Chiba Prefecture, which is part of the Greater Tokyo Area. It was the biggest and most important airport serving Tokyo back then, before it was replaced in this function by Haneda Airport.
		"Mount Tengu" from Chapter 13 - 24 (Yaiba Volume 2, Chapter 4 - Yaiba Volume 3, Chapter 5) Yaiba, Kagetora and Shonosuke are abducting Sayaka to and on which Miyamoto Musashi has been living for the last couple of centuries is a real mountain on the border of the cities Chino and Koumi in Nagano Prefecture.
		In Chapter 15 (Yaiba Volume 2, Chapter 6), Takeshi Onimaru is awakening the Eight Demons in a cave at Mount Fuji, which is a real volcano on the boundary between the Prefectures of Shizuoka and Yamanashi and within sight of Tokyo.
		Onimaru forces his entry into the Kokkai-gijidō, also known as the National Diet Building of Japan in the district of Nagata in Chiyoda Ward of Tokyo to take over the government of the country and remodel the building in his image of a demon castle, which he uses throughout Chapter 17 - 61 (Yaiba Volume 2, Chapter 8 - Yaiba Volume 7, Chapter 2). So, yes, Onimaru's castle is technically a real building - as this, it's one of the more important places to pinpoint the location of the fictional Yaoya District and the mansion of the Mine family, since it's pretty close to the castle.
		Kokura Station from Chapter 40 (Yaiba Volume 5, Chapter 1), at which Yaiba, Sayaka and their friends try to escape from Kojiro Sasaki to Tokyo, is a real train station in the [url=https://ja.wikipedia.org/wiki/浅野 (北九州市) Asano District]_(jp) of Kokurakita Ward in the City of Kitakyushu, situated in Fukuoka Prefecture.
		Sayaka, Kagetora, Gerozaimon Geroda and Namako-Otoko arrive in Tokyo at the Marunouichi Building of Tokyo Station (pre-renovation status) in Chapter 42 (Yaiba Volume 5, Chapter 3), which is also named as such. It's location is the Marunouichi District in Chiyoda Ward, Tokyo. They disguise themselves and instantly go to the Mine house by foot afterwards, implying that Sayaka's home is relatively close to Marunouichi - another hint that Yaoya Town is around Chiyoda.
		The twin tower building in central Tokyo Onimaru is about to destroy in Chapter 216 (Yaiba Volume 21, Chapter 7) is the Tokyo Metropolitan Government Building in the Nishi-Shinjuku District of Shinjuku Ward.
		The luxurious home of the Kurogane family (or to be more specific, the house of Yaiba's sister Moroha and their mother Michiko) is modeled after the Palais du Luxembourg, in real life to be found at Rue de Vaugirard 15 in the 6th arrondissement of Paris.