You’ll only cut one-fourth to one-third of the way through the branch. There could be tons of reasons why you need to prune your trees. Make the first cut on the underside of the branch, about six inches from the tree trunk. Learn How to Prune Tree Branches With Some Easy Steps. Pruning tree branches in the right time, in a right way, is as important as planting a tree at right time and the right way. Selectively remove branches to thin out the tree canopy, or top of the tree; Steps to Easily Prune a Tree. Branches break and fall off. Trunks fork in ways that foreshadow future instability. The crown grows so thick that light can't penetrate, air can't circulate, and, in the event of heavy wind, the tree may catch too much of it and become uprooted. Branches shoot out at eye level or lower. Their stubs decay and admit disease.