If you don't have any blank media to temporarily store the data that you want to save, another alternative is:
1. Create a small partition large enough to store the files you wish to keep on your HD.
2. Move the files you wish to save over to the new partition.
3. Format the original partition.
4. Move the saved files back to the newly formatted side of the HD.
5. Remove the partition you've created if you wish (which should contain no files now), and you're done.