Well... i have an idea about how you could do this..

You could copy the files to a new folder (or set of folders) from a command prompt using XCOPY e.g.

XCOPY C:\source\a*.* C:\A_Files

would copy all the files from the source folder which begin with "a" to the folder "A_Files"

You would need to repeat this to get all the files, and it could take a while with that many files, but it should work!

Hope this helps

Rich