You should first diagnose what type of fin rot they have.
Fungal fin rot usually eats away the tail in a consistent area, white cottony areas are also usually present at the tips of their fins. JFC is or JFE is the best treatment.
Bacterial fin rot is usually inconsistent and attacks random areas, often making the tail look frayed at the edge or create holes in the fins. For mild cases, you can use Maracyn + Maracyn-two in combination. For more serious cases Tetracycline, Ampicillin and Penicillin may be used.
Water must be kept very clean at all times and salt baths will help a lot.