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Plug in both USB pen drives and type: fdisk -l as root in terminal to see what their device names are. If they appear as /dev/sdb and /dev/sdc, type in a terminal: dd if=/dev/sdb of=/dev/sdc conv=notrunc.

To make an image of the entire drive including MBR (boot files), type in terminal: dd if=/dev/sdb of=/path/to/destination/image.dd conv=notrunc. To restore the image to a new drive which is seen as /dev/sdb: dd if=/path/to/image.dd of=/dev/sdb conv=notrunc