wow that sucks... definitely post a few pics and make sure it is coumnaris, I've heard from people who got caught up with columnaris. Definitely treat quickly IF you are sure, as it can kill your fish overnight :/. Also for my filter intake I bought this sponge prefilter by fluval and i LOVE it. It reduces the intake and I also like to squirt their flakes on it. The suction keeps it in place from swimming all over the place and the mollies get a kick out of scrubbing the sponge down. here is a link to the product I definitely recommend it.
It will squeeze (lightly) around the intake and will stay in place with help from the suction. I have it on my aquaclear 30 and it is awesome.