[CentOS] Need a Centos 6 USB hard drive recovery procedure

My 15GB backup USB drive somehow got "corrupted" such that
a "chkdsk /f E:" on WinXP removed the file allocation table
(or whatever) making the NTFS drive appear empty.

I tried Windows Recuva freeware to recover the files, and
it has been working for 24 hours; but it has dumped about
65,000 files into a separate flat Windows directory.
 http://www3.picturepush.com/photo/a/12892041/img/12892041.jpg

Since none of the files were deleted or written over, is
there a method on Linux that will simply recover the missing
file allocation directory structure instead of dumping a 
hundred thousand files into a single directory?