agreed with david, your best bet is to cut out as much of the diseased/rot/fungus-whatever tissue to save the healthy. do not skimp when you're cutting out, sacrifice some of the healthy tissue in the process. for this type of cutting, an exacto knife or razor is very effective.
i'd do the procedure in another container (preferably filled with the same tank water to limit shock). then closely examine the area, first scraping away the infected parts and then cutting into any discolored areas, and then finally a little further in to make sure you've removed all infected tissue.
a picture of what you're dealing with is also helpful to us to help you.
usually, after such a procedure i like to dose a little lugol's or kent's tech I. but that's just my pers pref. i use them more as an antiseptic in this instance than a coral growth additive or similar. hth