If you cut the branches off beyond the meristem, the swollen area where the branch and trunk meet, which is the proper way, then leave it uncovered. Regardless of what you did DON'T cover it with anything. Research shows that using any type of covering does greater harm to the survival of the tree than covering the wound (cut). Throw away that 50-60's idea that still promulgates the plant world.

I'll agree with petzold, just to give you more confidence that the advice is sound. Tree and branch wound dressing is rarely a good idea. There are a few instances when the practice is called for, but this is not one of them.

Both of the above responses are right on target, but one of the Tree Forum regulars, Spruceman, has come up with some very promising ideas that might benefit you. I will provide a link below. This is one of the best novel ideas I've seen from Gardenweb, and I've been around for a loooooong time.

Here is a link that might be useful: Preventing Wood Rot in Trees--Liquid Copper Fungicide