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Yes, it is highly recommended to remove tree stumps. Leaving them in the ground can lead to several problems, as they are not only unsightly but can also reduce your property's value. Stumps can obstruct landscaping plans, make mowing difficult, and hinder new growth. More importantly, they are prime breeding grounds for pests like termites, ants, and mice, which can spread to your home and cause costly damage to its wood and foundation. Stumps also attract fungi and diseases that can infect other healthy trees and plants in your yard. As a stump decays, it might sprout new, unwanted shoots. While removing a stump is an investment, it prevents these potential issues and enhances the safety, health, and appearance of your landscape.

Aside from removing dead or diseased branches, you should prune your trees somewhere between every one and three years. Some people—particularly commercial farmers—prune their apple trees yearly to produce higher yields. This is the best way to promote tree health. That said, the average homeowner can get away with hard-pruning their mature apple tree every other year or every three years. 

Any tree that needs to be pruned should be pruned to remove dead branches at least once a year. You may need to prune far more often if you’re trying to maintain a certain shape or to save a tree that suddenly becomes infected.

Carefully pruning small roots no thicker than three inches in diameter won’t harm the tree. However, cutting larger roots may impact the tree's stability and nutrient absorption. It's advisable to consult an arborist or tree care professional to evaluate the root's size, the tree's health, and the potential impact of cutting. Proper tree pruning techniques and timing can minimize damage, but larger root removal may necessitate expert guidance to avoid compromising the tree's overall health and stability.