Apple trees, like many other trees, are susceptible to black rot, a canker disease that occurs only when a tree has an open wound. The best way to take care of this problem is to cut out the affected area and fill it with a pruning paint. While pruning paint generally does not protect the tree from future problems, it does make it more aesthetically pleasing. When done correctly, a corrected black rot problem is almost undetectable.
Locate the areas on the tree with black rot. The bark in the affected areas will be much darker than the rest of the bark.
Slice open the suspected rotted areas with a sharp knife or the blade of pruning shears. If the flesh of the tree is brown rather than the normal white or green, it is a sure sign of black rot.
Cut the black rot out of the tree with pruning shears or a sharp knife. Remove all the infected area to reveal white or green flesh.
Cover the open wound with pruning paint according to the product's directions.
Repeat for additional rotted areas.