Why is my bettas fin rot not healing

My betta has very severe fin and tail rot. I have been trying for over a month to help him heal, but nothing seems to be working. He lives in a tank with a filter. I do regular (biweekly) 25% water changes. First I tried Maracyn and Maracyn-Two in powder form. When these did not work, I tried Melafix, which I am currently using. His tail seemed to be growing back, but when I moved him out of the tank to do a water change, his fin was destroyed again. It seems like there is some regrowth now (fluffy white at the end of his tail), but I am afraid it will be damaged again, and I don't know why it's taken so long for it to start growing back. The directions on the Melafix say that I might want to remove the activated carbon from my filter, but I use a Penguin-mini filter, and the activated carbon is inside the filter pack. Please help! My poor Morty is in trouble, : (

Most 'fungus' infections are opportunistic secondary infections that take hold on damaged skin. There are a few things to do.

1. Make sure you are not overfeeding - that is the number one cause of fish death. Excess food rots and creates large amounts of bacteria and ammonia. This ammonia can burn the skin, removing the fishes protective slime and making it easy for bacteria to get into the wound.

2. Get your PH checked, for the same reason as above extremely acid water can burn the skin and lead to similar conditions. Are you using bottled water to fill the tank? If so be careful. Distilled water or some other similar processed water may have no minerals to buffer acidity. What that means is that the fish waste and respiration can make the water acid very quickly. It is ok to top off the tank with distilled water since minerals don't evaporate, but if you are taking out and filling then you either can use treated tap water (removing the chloramines) or spring water (or carbon filtered, ozonized) which still have some minerals - distilled water is pure water, no minerals.