Yes, calibre has very powerful functions to save books to folders and files named after metadata fields. Even custom metadata fields that you create yourself.
Save to disk and adjust the save template.
Also for setting metadata from filenames.
And even for changing metadata on the fly to allow you to add series information to the title if the book format doesn't support series information in dedicated metadata fields (mobi).
And lots more...
Have a look in the manual!
http://manual.calibre-ebook.com/