Prune arborvitae shrubs by starting at the top, working around the tree and avoiding pruning anything but green foliage. The exact timing and type of cuts depends on the type of pruning.
To prune the arborvitae for height or top-down, start in the late winter before the sap starts moving throughout the shrub to reduce shock to the plant. Start at the top, working around the tree, and cut away the limbs above where the branch and shoots merge. If hard pruning the shrub down to the ground, start in the early spring before it starts to flower. Keep a few of the main branches, called the leaders, and remove the secondary limbs. Trying to remove a large branch that is more than 18 inches tall can tear the bark. Prevent this by removing the branch in smaller sections.
Trim a arborvitae in mid-summer, giving the plant plenty of time to grow and recover after the pruning before winter. Thin out the secondary branches by cutting close to the junction of shoots and branches. Unlike top-down pruning, this encourages the branches to grow upward while allowing airflow throughout the plant. Prune diseased and damaged branches by cutting the limbs off far below the lowest evidence of disease or damage. Disinfect the pruning shears immediately before and after removing diseased limbs.