I recently had the need to clone a bootable USB flash drive, inside which there are multiple partitions.
There are many programs to create clones of hard drives, but these do not work with the USB pen drive.
Searching the net I found the very useful "USB Image Tool" does just that in my case, this differs from the others for its peculiarity to create an exact disk image of USB devices, including iPod, in an extremely simple and occupying very few resources, weighs only 180Kb!
You can download it from here:
http://www.filecluster.com/downloads/USB-Image-Tool.html
