You can''t (easily, and you don't need to). Don't attempt to use a different file system. Just use NTFS (better and sfaer than FAT32, but FAT32 will work for files smaller than 4 GB's) and copy the files. You can use the partitions you already have, or make a new one with third-party software, but that is a risk to the data unless you have another copy (which you should - data not backed up is data you don't want to keep).
If you are backing up DVD's, make iso images of the disks with ISOBuster, UltraIso, or similar. But again, since FAT32 is such an oild file system, it only supports files up to 4 GB's, so a full DVD will not fit.
