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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.

In nature, there are many things that can cause a tree to die, including diseases, insects, and natural disasters such as fires or droughts. Non-natural methods of killing a tree include herbicides or manual intervention, such as cutting it down. Consult a tree removal professional about your options for naturally killing a tree.

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. 

It depends on the type of tree. Typically, late spring on the cusp of winter is ideal for trees about to emerge from dormancy and produce new buds. That said, late fall is ideal for certain deciduous trees prone to bleeding sap. Avoid trimming trees in early spring, when they’re prone to disease.