If you are marking them as 'found' as you find them, then you can remove them by deleting the field_notes.txt file (or something equally obvious, I forget the correct name.
This should remove them for you.
Is there any reason you actually want to delete them though?
I only want to delete them so that I use less space on the GPS, that's all really, plus if I've done them then I don't really need them on there any more (just in the same way you'd remove a waypoint that you no longer need). So just to remove the unnecessary clutter.