when you install Win2k you have the option to repartition. After its done re-partitioning it will automatically format the drive to whatever filesystem you desire between NTFS and FAT
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There's really no 'commands' per say, as there is no command prompt
The install process will give you the necessary options of deleting the current partitions, then create new ones and then after that part is done it will ask you what file system to make the system partition. Once you've completed the install and are in Win2k you can use disk management to format any remaining partitions