Popeye is usually a secondary infection. More than likely your molly has something else wrong and the popeye is a symptom. It's impossible to diagnose or suggest treatment without more info. Can you post pics? Water stats? Tank size and occupants? How often do you do water changes?
Normally popeye is a bacterial issue. Fluid builds up behind the eyes and pops it out. Use bacterial meds. Many medicines by mardel however treat popeye, mouth fungus, and tail rot all in one. Those seem to be based on fungal treatments but they work.