To produce healthy fruit, peach and nectarine trees will require yearly pruning. The Vase Training Method produces a vase-shaped tree consisting of 3 or 4 scaffolds (main branches) of equal lengths and no central leader (vertical growing top central branch).
When To Prune Peach and Nectarine Trees
You'll want to prune peach and nectarine trees in late winter before new leaves begin to emerge. This is typically February, but adjust this time based on your local weather. At this time it will be easier to detect buds that have been damaged by cold weather. If a flower bud looks as though it has been winter-killed, cut it off. Also cut off winter-killed limbs that have wrinkled bark.
How To Prune A Young Peach or Nectarine Tree
If you have purchased bare root trees follow the instruction below for intitial pruning at time of planting:
Small Bare Root Liners: These are single-trunk "whips" that usually have no side branches and should be topped at 30 inches above ground at planting time. The shoots that will become the main scaffold branches of your tree will usually emerge on the trunk within 4 to 6 inches below the cut.
Larger Bare Root Trees: 
If the bare root tree is branched when it comes from the nursery, select three or four lateral branches growing with wide-angle crotches (greater than 45°) spaced evenly up and around the trunk. These will be your permanent main scaffold limbs. The lowest limb should be about 15 inches above the ground and the highest about 30 inches from the ground. If no desirable laterals are available, top the tree to 30 inches in height and cut out all side branches to a point where there is only one bud left on the branch. A shoot will often develop from these buds and may be suitable for main scaffold limbs.
Container-Grown: 
Many container grown trees that you purchase at your local nursery are 2-year old trees. I they were pruned properly by the grower these older trees will already have strong branches with wide crotch angles. During the first dormant season (winter), these branches should be pruned back (headed) to a point that leaves 6 or 7 buds on the branch. The height at which branched trees are headed depends on the size of the tree and the positions of good side branches. Remember, you will only be keeping 3 or 4 main scaffold branches. It's best if these are spaced evenly around the trunk. Remove any weak branches growing from the trunk and any suckers growing from the base.
