Under WinNT4, it was possible to do this using the RDISK /S- comand, which compressed the registry and placed a copy in the Repair folder, then you simply needed to expand it again to have a "cleaned up registry".
Under Win2K, the RDISK command was removed because the Win2K registry would not fit on a floppy for the ERD. What you can do is go to Accessories, System Tools, Backup, Create Emergency Repair Disk, and check Backup a copy of the Registry.
The backup copy of the registry will be placed in the repair folder. After this has been done, you can boot up to the Repair Console, and expand the backups from the repair folder and replace the registry with the "cleaned up version".