Flatworms are hard to get rid of. If you have acros you must blow them off everyday to minimize damage. Sanjay has a 500 or 600g tank with FWs and he has been able to keep his reef healthy despite having flatworms. Check out his thread on RC.
Are they like http://www.melevsreef.com/id/clear_flatworm.html
If so I believe that they are relatively harmless, they supposedly reproduce pretty fast but I don't think they target any corals like the aefw or the bigger ones. I see them in my tank occasionally but mainly on the glass they just scoot around doing i don't know what, and I really haven't noticed that many.
The small clear flatworm that is in that picture are very common in newly established tanks. They don't increase to plague proportions and seem to disappear after a time on their own. No treatment is necessary.