How do you plan to format it? If you are using a partitioning tool then you can just delete the partitions that have windows on them. If it's another HD completely then you can fdisk. From what I understand, nothing relating to deleting windows would affect GRUB or your linux partitions. Just be careful when using any partitioning tools when you have data that is needed to be kept, it would be a shame for you to accidentaly delete your linux partition(s) and have to start all over again. I would look at the commands for fdisk but I got linux on a dual boot system and am on XP now, so no can do on further instructions. Just look at the man pages for fdisk, and be sure you know what you are doing.
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