All of the locations used in the series – in the United States, France and England – are based on real places. In fact, so specific are the locations that it is possible to trace the journey of the twins and the Flamels across San Francisco, through (and under) Paris and into London.
A little while ago, hitmanjls, one of the moderators on Flamel’s Secret, the official fan forum, did just that, and created a marvelous visual tour of The Alchemyst and, more recently, did it again for The Magician, using maps and images from Google Maps and Google Street View. He then linked the images with text from the US editions of the book.
If you have read the first two books, it is well worth while checking out.