Answer: If the roots are from old trees that have been removed, that is if they are no longer attached to a tree, you can dig them out or have them ground down to wood chips. If the roots are still attached to live trees, you may have to design your flower beds around them.
The large roots near the trunk of older trees often rise above the soil level. This is the result of them growing in diameter over time. A small root, say "pencil-sized," growing a couple of inches beneath the surface goes unnoticed. As that root expands in diameter to the size of your arm it naturally pushes part of itself above the surface. Sometimes erosion from rainwater runoff contributes to root exposure. This does not hurt the tree, but can pose a problem when the area is covered with turf and needs to be mowed. You can add a couple of inches of soil once or twice a year, spreading it evenly over the area where roots are exposed. This will fix the problem enough so that you can easily mow over the area without damaging roots or the mower. Cutting roots is a drastic means of dealing with the situation. If only one or two roots is cut every few years, the tree may not be severely damaged, but will be stressed nevertheless. Also this practice to some degree weakens the tree's anchorage strength which may result in problems during a storm with high winds, so I don't recommend you cut these roots. Thanks for the question. Good luck with your trees!
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