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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.

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.

While the fastest way to kill a tree is to simply cut it down, there are several other methods to choose from. You should hire a professional tree removal service to cut down a tree to ensure your personal and property safety. Some slower but effective options include treating or grinding the tree stump or using a basal bark treatment. 

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.