Most nectarine trees are trained into an open-center or vase shape, with four to five main or scaffold limbs shooting up and out from the main trunk. Pruning a young nectarine tree into this shape takes several years, but the gardener's rewards are numerous: higher fruit quality, improved tree heath and greater light penetration into the canopy. Pruning begins when the young tree is planted.
Cut a newly planted nectarine tree back to a height of 28 to 30 inches. If your tree has branches already, you can trim these back almost all the way, leaving two to three buds on each. Then let the tree develop until the first winter after planting. Once frost danger has passed but before the tree begins to grow, it's time to prune.
Select four to five branches that shoot out and up from the main trunk, making a 30- to 45-degree angle with the tree trunk. Anything tighter than that is too close to the trunk. These branches will be your scaffold branches. Cut off any offshoots of the scaffold branches, but leave the branches alone otherwise.
Trim off all other branches, including those that grow at a tighter or looser (closer to 90-degree) angle to the trunk. Cut the branches off at the intersection with the trunk, but don't cut into the trunk. Prune away branches that grow lower that the scaffold branches plus any suckers, or growth originating below the graft union at the base of the young tree. Let the tree grow until the following late winter.
Remove any suckers and low-growing limbs in the same manner as before. Eliminate any growth between the scaffold limbs and the trunk of the tree. If left to grow, this will produce shade and will clutter the tree canopy. Trim back the tips of your scaffold branches if necessary so that all are the same size. At this point, your tree should be well established in the vase shape.
Prune every late winter thereafter to remove suckers and wood that grows vertically up (or down). Remove weak shoots that are too weak to hold fruit once your nectarine begins fruiting.