Looks to me like you plan on performing this subtraction on a supatched object. Using boolean operations in this case will cause you a ton of headache.
The reason is subpatches can only contain three and four point polygons. When you perform your subtraction you will be left with a large number of n sided polys.
The best way to make those holes is manually. Drag the points around on your surface to form the shape you need and delete the uneeded polys.
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