You could use GParted or the command line.
Find the partition you want to format:
sudo fdisk -l (lowercase L)
For example, let's say your internal drive is showing up as sda, and the external usb as sdb, and the partition you want to format is the second one, sdb2. You could use mkfs to format as ext3:
sudo mkfs.ext3 /dev/sdb2
Or, GParted has a GUI.