Cloning a USB pendrive to another is easy ... in linux ...
use blkid to find the two drives
example output :
origin = /dev/sdd
destination = /dev /sde
the command is :
dd if=/dev/sdd of=/dev/sde bs=4M
to see dd's progress, find the pid of dd (in another terminal)
ps -a | grep dd
add a 10 second timer to ask dd how it's doing ... (in another terminal)
watch -n 10 kill -USR1 {pid of dd}
and dd will spit out it's progress ... easy!
excerpts from :
http://linuxcommando.blogspot.pt/2008/06/show-progress-during-dd-copy.html