To do a clean install, either boot the Windows 2000 CD-Rom or setup disks.
The set of four install disks can be created from your Win2k CD-rom; change
to the \bootdisk directory on the cd-rom and execute makeboot.exe (from dos)
or makebt32.exe (from 32 bit) and follow the prompts.

When you get to the point, delete the existing NTFS and or other partitions
found. After you delete the partition(s) abort the install, then again
restart the pc booting the CD-Rom or setup disks to avoid unexpected drive
letter assignments with your new install.

During Windows 2000 setup, at some point, will want to confirm the previous
operating system for the upgrade; at that point you'll simply insert the
qualified product install CD for it to verify. Then the install will
proceed.