Folders over VPN

I have an NT server being accessed over VPN (DSL and Frac T1) by 4 small (4-6 PCs) regional offices. On most VPN activities speed is acceptible. One area is not. I have a drive 650 folders in the root and a total of 16,000 folders and 22,000 fileswithin. Total size is 8.6 GB, mostly Word, Excel and CAD files. This drive is very slow to load over the VPN. I don’t have the option of eliminating files and folders. What I could do would be to set up three folders in the root called a-e, f-n and o-z and then put the 650 folders presently in the root alphabetically into the appropriate folder. Do you think this might speed up access over the VPN, 3 folders in the root instead of 650.
Thanks,
Mike