It is IMO darn near impossible to "eliminate" flat worms. Their populations naturally rise and fall, you may not see them, but sure enough where there's one there's a hundred. Do as reefD says and siphon them out one by one with tubing, or suck'em up in a turkey baster. Then look for natural alternatives vs. chemical warfare, velvet nudis, peps, canary wrasse, six line wrasse, etc.