one freeware program that is useful for identifying open files and handles is Process Explorer.
Using that, you can search for a file (or folder name) and it will show you all the related files, handles, registry info that is open relating to it.
I use it all the time when windows locks up a file and i can't delete it.
Its actually distributed by Microsoft now, so its safe to use on your Windows 2003 server.
http://technet.microsoft.com/en-us/sysinternals/bb896653.aspx