Hi
Formatting wont do it I'm afraid, neither will partitioning. U3 and some others emulate a CD in their firmware - which means as far as Windows is concerned it's pretty much a separate device.
Some of manufacturers provide tools to manipulate the vCD - can't recall whether U3 do. M-Systems (who designed the U3 system and then partnered with Sandisk to try to poularise it) used to provide such tools as a downloadable SDK. But we are going back quite a while.
Drives are so cheap now why bother with it?
HTH