Prune to one central leader while the cypress tree is young. The central leader is the uppermost part of the tree that grows straight up. If the tree has two parallel leaders, cut one off where it joins the main branch stem. If the tree is damaged, it might grow another leader, but it should be removed.
Cut brown or damaged growth back to the nearest healthy shoot with hand pruners.
Remove a few of the lower branches at the point where they attach to the main trunk, if you would like a little extra clearance under the tree. Remove them when the tree is 8 to 10 feet tall. If you remove more than the lowest whirl of branches, the tree might develop an unappealing, lollipop shape as it grows taller.
Remove branches split by heavy ice and snow at the point where they attach to the trunk. After removing a branch, close the gap by tying the remaining branches close together using rubber tree ties. If the branch is bent but not split, remove as much of the snow and ice as possible and tie up the branch.
Plant the trees 3 feet apart to provide a dense hedge or at the desired spacing as foundation plants.
Allow the trees to grow 1 foot past the height at which you want to maintain them.
Cut off the top 18 inches of the tree in early summer.
Prune every year in early summer, cutting out the top to the desired height.