Windows 7 virus removed shortcuts and folder permisions

viruswindowswindows 7

A friend's machine has become infected with a virus which seems to have messed up his Windows 7 set up quite a bit. This computer only has one user. When he logs in all desktop icons are gone and all shortcuts under All Programs are missing (the folders are there but not any shortcuts to the program). The programs and files are still there as far as I can tell.

1. I can start typing "itunes" in the Start Menu search box – the program will show up and run.

2. The My Documents folder is empty even though there should be a number of Word documents and folders. The strange thing is that when I run WinDirStat under C:\Users\Ashley\Documents I can see all the missing folders and files but when I try to explore from there it is empty.

The situation is like I'm logged in as Ashley but Windows has reset all the basic settings, e.g. where the My Documents folder is.

At this stage I just want to reinstall Windows 7 but I first want to copy the My Documents folder to an external hard drive. Windows Exporer / My Computer won't let me see the files even though I know they are there after using WinDirStat. I thought I might be able to see them from a Command Prompt but that also shows an empty folder.

Does anyone have any ideas what software I can use or steps I can take to copy the files, or perhaps even some insight into what might have happened?

PS. the virus was detected by Windows Security Essentials (Norton missed it) and consequently deleted.