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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.

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. 

Yes, cutting a tree's roots can cause it to fall, particularly if major support roots are severed. In extreme cases, trimming roots can affect the tree's structure and stability. Many crucial roots are located just below the soil's surface. If you make severe cuts to roots more than 2 inches in diameter, you risk impacting the tree's water flow and its ability to withstand severe winds or storms. Even cutting roots less than half an inch in diameter under or outside the tree's canopy can cut off its water supply, causing it to decline, die, and eventually topple.

Tree pruning is a common and helpful tree maintenance technique that involves carefully cutting and trimming unwanted branches so that the tree can continue to grow and thrive. Pruning is done carefully and intentionally. Tree topping is a frowned-upon method that involves removing and cutting most or the entirety of the top of the tree, including structurally important branches.