Personally, I would wipe the disk first and then format it.
To wipe a disk I would use the command
sudo dd if=/dev/zero of=/dev/sdX* bs=1M status=progress
*replace sdX with the target drive location.
To get a list of drives and their partitions run
Ensure that you list just the drive code eg mmblk0/sda and not a partition on that device eg mmblk0p1/sda1
This will overwrite every bit on the disk with 0s however it may take some time. But at the end, there will be nothing on it.
Once the drive has been wiped you should be able to format it as you wish.
I would generally use the
mkfs command as suggested in Lorenzo's answer. However, if I were to use a graphical tool I would recommend gparted
The 'if' is the part to be copied to the disk and the 'of' is the location to which it is to be written to, the status part means that it will show the progress of the operation as it goes along.