I believe you can use Salifert's Flatworm Exit in the tank. The only prob I remember reading is that when the flatworms die, they release a toxin, so when you kill a whole bunch of them, that's a whole lot of toxin in your tank which isn't good for other corals and fish.
I have read that you should try and pick off as many as you can before you decide to use the FW Exit.
Hopefully someone else with some more experience with this can either back me up or can tell me where I am wrong at.