Not that I know of (unless flatten will do it - it deletes a folder once it has successfully moved its recordings to the top level, but I'm not sure it acts on an existing empty folder). However, it's no great shakes to go through the WebIF media browser and tick all the folders you want to delete (or tick all and then untick what you want to keep) and then delete them all on one go. You can do similar on the Standard User Interface - use the red button to tick/untick, green to tick all, and then OPT+ to delete the selection.
The question in my mind is: why are you getting left with empty folders, and how to stop it. Is it the case that you have series recordings, and then when you have watched and deleted the programmes you are not then deleting the series folder? Would flatten not suit you, which effectively counteracts series filing by dumping all recordings into My Video (and then the oldest recording - ie the next thing to watch - is always at the bottom of the list, which you can get to quickly by moving the cursor up from the top)?