For doing a clean install, also boot the Windows 2000 and install the CD-Rom or setup disks. The set is of four install disks which can be produced from the Windows 2000 CD-Rom; modify to the \bootdisk directory on the CD-Rom and implement makeboot.exe (from dos) or makebt32.exe (from 32 bit) and go after the prompts.

When you are able to get to the point, by deleting the obtainable NTFS and or any other partitions found. After you have deleted the partition abort the install, then again restart the pc by booting the CD-Rom or setup disks for evading unanticipated drive letter assignments with your new install.