How many do you have in the tank now, compared to before? Is it just an annoying 100 or so, or do you still think you have 1000s and 1000s?
The canister filter only needs 2 cups of carbon, max. That's enough to treat 200g of water, which is major overkill.
You should take a few out and put them in one gallon of water, add a drop of medication and move the water with a spoon or something. Keep adding a drop and stirring to see if you get a reaction out of them. Whatever number of drops affects your flatworms, that's how many drops per gallon you should use.
All filtration should be off for the dosage. Leave all the pumps on. No GFO, no biopellets, no skimming, no carbon. Within 5 minutes you'll see them dying. Siphon them out with airline tubing. You'll see some dangling off a weblike thread, and you may see 5, 6 or 7 of them on a strand of web. Siphon them out as they die. After a total of 15 minutes, start up the canister filter with carbon, and your skimmer. If you want to do a 10g water change, it won't be a bad idea. You can restart the GFO and biopellets next, around the 30 minute mark.
Here's my original write up, which is rather mild with the dosage and reaction time. I think you can be more aggressive in getting the water cleaned up, to remove the toxins they release. http://www.melevsreef.com/flatworms.html
Honestly, before treating you want to have siphoned out the bulk of them. 75% or more should be gone, the less there are, the better.