Hi ladcmd,
You scan it like any other partition of your OS. It is just like scanning a floppy disk or a cd, you can also scan from inside the usb storage device, if you have downloaded a recent scanning tool there, DrWebCureit or Stinger.exe for instance, or you can even scan it from another OS, just go to the partition there, lets say drive F, no sweat.
greets,
polonus