With Calibre (calibre - E-book management), when you import ebooks to your library, it will automatically copy them and create the appropriate directories. It uses metadata from the file to do that. This will result in a tree-like structure which might be what you want.
It follows this renaming scheme :
Library
> Author Name
> Title (Series Name)
> Title (Series Name - Author).epub
The first 3 are directories. The last one is the file itself. I put epub as an example but it can be any ebook format.
I've never tried to change this directory structure. If you feel the need though there's a thread about that on the calibre forums (Want to change the folder structure of the Calibre library? - MobileRead Forums)
Other than that you could try websites specialized in ebook management like Goodreads (https://www.goodreads.com/). There's no real "map structure" in goodreads though that I know of, except for tags with what's called a tag-cloud (http://en.wikipedia.org/wiki/Tag_cloud). You can define your own tags though so it might be what you are looking for.
