If the flat worms are living there due to the accumulation of nutrients in the water, do what every aquarist does to combat the problem, a water change. Take a turkey baster and remove some whater, and add fresh water to replace what you removed. The fresh water dilutes the nutrient rich water that you have in there right now. Do that several times (once every few days) and see if that alleviates the problem. And by all means continue to remove them manually if you can.