The nudi can work, but once the food source is out it can starve, I believe. First, what color were the flatworms? I believe there is 1 type that isn't harmfull. I cant remember which right now. Do a search for flatworm exit, if it is the type that needs to be taken care of. From what I have read, if you see a few then there is most likely more and can become a problem. There was a step by step thread on how to do this in the reef forum a good while back (over a year ago). If you would ever use this, please ask questions beforehand---you will need to have a good understanding of the do's/dont's and how too's. Also once you do have them under control, always dip anything new before adding.
Humm...I just reread your post and you are cycling. Are you sure they are flatworms, not pods? Reguardless a nudi is too fragile for a new tank, IMO. If it is flatworms and you look into flatworm exit, you may have a little more leway (sp) on mistakes if nothing is in the tank. Can you get a pic or describe what you are seeing? Little info on the tank---what do you have in it so far? How old?