That one is a tough one. I wouldn't personally suggest deleting the hives. I think it would be smarter to delete all the fonts under Control Panel ¦ Fonts, Reboot your machine and then readd them in again from an NT CD. (you probably really don't need to reboot but it is advisable to be safe) However if you really just want to delete them from the registry you can kill the pointers at:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Fonts. You might try just deleting them first, rebooting and then look in that key and see if it removed them.