Actually Jungle Anti-Parasite food is the one I would try to feed to the fish. It has Praziquental, Levamazol & metronidazole, should take care of most worms & internal parasites. <Parasite Clear is one you add to the water, good for external stuff like ich, not too good for worms.>
I don't know enough about puffers to say for sure. Certainly in goldies, if you see a worm sticking out, I would be sedating the fish & remove the worm with tweezers. Also, removing the worm & looking at it will aid in diagnosis, as some worms (like anchor worm) need different treatment. <Anchor worms are actually crustaceans so won't be killed by the anti-parasite meds --- which are targeted towards true worms (helmeths).>