Are you diagnosing from a book?
Cotton Wool disease, if that is what it is, is not caused by fungus at all, its caused by bacteria attack (edit: Flexibater if I can remember the spelling!).
You should look on the list of symptoms any med treats before using it, cotton mouth disease or fllexibacter should be listed. Fungus cure may be ineffective.
To tell if is fungus or not, what I do is this:
Take the fish out of the water using a very soft net, bag or better yet your hand.
Quickly examine the diseased area. If it is fungus, the 'cotton' look should have almost dissapeared as fungus loses its form out of water. If it is still prominent, it is probably bacterial or a tumour.
In either case, 10% daily water changes with water aged overnight is essential for a quick cure.
Ken