We bought our pecan orchard when the trees were five to six feet tall. They had been neglected for several years and had branches growing on the lower trunk. With the hope (and the notion that those lower branches produced pecans, too) that we could turn a profit from our pecan crop, or at least break even, we were cautious with our pruning for the first several years. We 'worked our way up' the tree for the first three years, removing the branches from the ground to a height of three feet the first year and removing another two feet of growth each of the following two years. This prevented throwing the trees into shock and allowed top growth to offset the lower branch removal. We were successful in producing a crop each year by following this method.
Pruning is in fact training your tree to grow the way you want it to grow. Pecan trees must have ample sunlight to produce a crop. With this in mind, you should prune to allow the upper branches to spread and to take in as much sunlight as possible. Many pecan experts say a single vertical trunk is essential. We pruned our trees to achieve this for the most part. We pruned one tree close to our house into a 'vase' shape because we designated it the 'climbing tree.' Approximately two feet from the ground, it splits into three 'trunks' forming the vase shape. It is a beautiful and well proportioned tree, and our kids have always claimed it as their tree. So, when it comes to training a young tree, you can decide whether to prune to make it become 'just a tree' or make it an eye catching part of your landscape. Just be sure you start out with a plan and carry it out throughout the years.
While mature trees will require annual pruning to an extent, your major pruning comes during the first ten to fifteen years of the pecan trees life. Keep in mind during those years that you need access to the orchard floor beneath your tree. You will spend considerable time underneath your tree, watering, fertilizing, controlling weed growth, and oh yeah...picking up pecans. When you are able to prune your tree's lowest limbs to a height just above your head, your major pruning chores are almost finished. There should be no need to prune the lower branches any higher than your head. You might keep in mind that someday you may be bringing in the heavy equipment (harvesting equipment) and be sure the shape of your trees will accommodate these machines. Other than that, your biggest pruning chores are complete.
Mature pecan trees will enevitably require annual attention. Small branches will grow downward in search of sunlight, and limbs bearing a heavy pecan crop will droop and continue a downward growth. The removal of these branches should be the only pruning you will need to perform on mature trees. Again, your goal is to be able to walk beneath your tree without a branch scraping your face!
Occassionally an upper branch will die and need to be removed. I suggest you purchase a telescoping tree saw/lopper to handle these problems. The cause of these higher branches dying range from high wind damage, freeze damage, disease, and improper care of your tree. I highly suggest you remove any dead limbs from your pecan tree as soon as possible to avoid the possibility of disease spreading throughout your tree.