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YOU CAN'T.
Now that I have your attention, the problem is that the C: drive cannot be re-formatted as long as the operating system is using it to run itself. You would have to boot to the CD or if you want a truly clean installation, I'd use a Win98 boot floppy and fdisk, delete the non-DOS partition and start over. You could fdisk again and create a Primary DOS partition, format it FAT32, and install Win2000. It could be converted to NTFS later. Or after deleting the partition, you could boot to the CD and start installation from there.