It should be OK at that part of the install from CD that asks you to select the destination of the O/S to delete any existing partitions (all of them) and then create new partition(s) and re-format the drive. Then proceed to install the O/S.
However
If you want to err on the safe side, then download the drive manufacturers disk utility program and perform a 'zero fill'. That procedure will not only 'unformat' the drive so you have to reformat it, but also erase any nasties (and everything else) on the drive.
If it's a genuine Windows 2000 installation CD, it will be bootable. You will probably need to alter the drive boot sequence in the BIOS. Usual default boot sequence is floppy first, than first hard drive. Alter this so CD-ROM boots first. During the installation process it will ask you where you want to place the system files. It is at this point you can select deletion of partition(s), format type etc.
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