Whoops. I forgot to add what I would do. If i'm going to be doing multiple layers with that intention, I would first "create a new set" and do all my layers in that set. You can then drag that set to the "create a new set" icon and click the eye to the left of the first set to make it invisible. With the new set selected (highlighted) press Ctrl-E (Ctrl-E is also "merge layer set" when a set is selected). It merges all the layers in the new set and removes that new set folder too. Filter can then be applied and you still have the originals there untouched.