When you say your water tested fine does that mean Ammonia 0, NitrIte 0 and NitrAte less than 10ppm? What's the temperature in the tank? What other tankmates do you have with the molly?
As to the treatment with MelaFix, I haven't had good luck with that. I know a lot of smart people who have, and I know Jack Wattley recommends it, but it just hasn't done the trick for me. I don't remember it saying that it even treats pop-eye, but if it does then swell.
Just follow the directions on the bottle.
When you have a sick fish, it's always better to quarantine them to prevent spreading the disease.