I'd like to find out how to do this, too. Not a big deal, but somewhat annoying in that the menu shows everywhere you've ever gone for as long as you've had the program installed to try and pick up a video file to burn. And the list keeps getting longer with most, if not all, of the locations being irrelavent any more.
I suppose that I could completely uninstall and reinstall it to clear this history, telling CloneDVD not to keep any previous info, but that's a pain.
Just a minor annoyance in an otherwise outstanding piece of software!!