Sorry, don't follow you.
Why on earth do you want to low level format the drive?
Are you sure you don't mean high level format instead?
If so, assuming the file system on the C & D partitions is FAT32 & not NTFS, just follow these instructions :
1. Boot from a boot disk containing format.com
2. at the a:> prompt, type: format c:/s/q
3. when finished, type: format d:/q