No really a big deal Jim more of an ugly eye sore than anything else.
Being in your frag tank is a good thing, as you may have the chance to catch them before they migrate.
Standard treatment is flat worm exit at 2-3X followed by carbon and at least a 20% water change.
With it in a system you can isolate I might do something a bit different though.
Depending on tank size, plumbing number of corals and substrate etc, I might:
Pull all the corals and rock to a tote for treatment. If the frag tank still has substrate dose it and do a 100% change or if no substrate just clean it good and add the new water.
Once that is back on line give each of your now treated and presumably clean corals a good rinse and inspection and add them back.
I'm headed to Hyannis in about an hour and I'll be there for the day. I'll bring some FWE so if you decide to we can meet.