Just pull them out and clean out all the crap and make sure the seals at the bottom of the cabin filter holder are clean. Oftern the build of of crap and age of the cars means the water can leak in even if its directed away from the top of the filter.
It never looks good when you cut all the rubber away. Id pay the 5 or 6 bucks and make it look nice and neat but then again, thats just me :)