Running CCleaner on a USB mounted drive

Is it possible to do this and if so, what is the command line information?

Bearrr

Do you mean from a usb or have ccleaner clean the usb mounted drive?

If the former, yes. use portable from http://www.piriform.com/ccleaner/builds . If the latter, not without making your own ruleset (winapp2.ini winsys2.ini)