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Generally, you’ll want to prune back the trunk by 1 to 2 feet each year to promote bushy growth. Doing so concentrates vegetative buds closer to the bottom of the tree, where you can easily harvest fruit. For side shoots that are a year old, leave at least six leaves. 

Never remove more than 30% of a tree’s foliage during pruning—even if your tree is really overgrown. Removing this much foliage at a time could kill your tree.

It depends on where you live—but in most areas, leaves begin falling in September and continue falling until January or February. Warmer regions, such as Southern states, may see leaves fall a bit later in the calendar year. It also depends on the type of trees in your yard and their maturity. 

In most cases, leaving tree roots underground is not a problem if the stump has been removed or ground below the soil. However, some larger roots may decompose, leaving dents in your soil. Additionally, some aggressive trees, including willows, oaks, elms, maples, and poplars may grow back from roots. Large aggressive trees with established root systems are more likely to grow back.

The best way is to start controlling tree height long before it grows too large, via careful pruning through the years. But that’s not always possible. If a tree has become too high or too large, use selective pruning to remove the most troublesome branches, one by one, without topping the tree. Gently shaping a tree like this can, over time, correct problems. You can also find growth inhibitors to spray on a tree to stop it from growing too rapidly, but use these sparingly if at all.