First, back up your files as if you mess this up, you can wipe out your whole pc's drive.
Insert the drive that you wish to format and start up gparted from the menu. Install it with Software Centre, Synaptic or Terminal if it's not present.
Gparted will open showing your first hdd, eg. " /dev/sda (*** GiB)", DO NOT FORMAT THIS ONE. Click the drop-down at top right and this will show any other mounted drives. Select the one you wish to format - make sure that the size you know the SD card to be matches the one that you select.
Right-click the drive you wish to format.
Hover over "Format To" then select the file system that you wish to install.
Click the green tick at the top and you're done.
Unmount the drive and remove.
If you are uncertain about any of the steps above, please note what you see (or take a screen shot), and re-post here. Use gparted with care.