File Structure Messed Up


I was using Virtual PC/Windows 2000 with a program that froze. After force quitting to get out of it, my folders were all messed up.

Whenever I opened an application it was like the first time opening it. My data files were not there, etc.

I have several folders of <my computer> in different areas, each one containing almost the same folders (desktop, library, documents, applications, etc.)

Is there some sort of program that I can run to re-organize the contents of my hard drive.

I need help!

iMac 17inch flat screen Mac OX 10.4