With Mountain Lion, you can now use the OS to encrypt disks other than the startup volume, assuming they are in GUID format. This includes USB flash drives and external Firewire/USB/ThunderBolt drives.
In the Finder, open a new window. Find your mounted (GUID) drive in the sidebar.
Control-click on the drive in the sidebar, then choose
Encrypt. You are now prompted for your password and a hint (which is required). You will get no feedback, so wait for a few minutes; the time depends on the size of the drive.
The drive should unmount and mount again. Once this happens, your drive is encrypted — via Mac OSX Hints