How to prune small trees Topping a tree is not good for the tree. You can prune back branches to make it smaller but you don't want to prune more than 10-30 percent of the tree at one time. You do not need to use a pruning seal when you prune. They do not keep bugs out and they do not stop the tree from bleeding. Black sealers actually heat up and kill off the trees cells. The wound actually closes quicker if you leave it alone. Often the prune sealers create a good environment for mushrooms to grow and they will start in the pruned area. The branch collar is a swollen area that jutes out from the trunk of the tree. You want to leave that in tact when you prune a branch off of the tree. It will protect the trunk and keep it healthy.