We start by mounting the drive (I know its already mounted but it helps me to explain), lets say /media/backup.
So lets create a folder to make the backup to:
sudo mkdir /backup/
Then we rsync your backup drive files to there:
sudo rsync -rvlt /media/backup /backup
Now you should have all the files that were in /media/backup in the /backup folder.
Now to reformat the drive (assuming backup is sdb):
sudo fdisk /dev/sdb
Hit the d key and delete first partition. If there is a 2nd partition then repeat.
Now hit n to add a new partition. If this will be the only partition just accept all the defaults.
Now hit w and enter to write the changes to the drive.
We now have an empty partition (sdb1) to be formatted in ext3.
To do this:
mke2fs -j /dev/sdb1
You should now be ready to go!