Instead, we need to use a combination of pie slice and the slice tool to make this happen.
First off, let's assume we're trying to chop a 4x4 tile hole into the top of this brush.
Now, go into the top-down view and start creating a pie of any size, as long as it's a perfect circle.
Adjust the center hole so it will be the size you want, so in this case I'm setting it to 4x4, which will equal 4x4 tiles.
You can also adjust segment number here, but don't go too crazy with it.
Now, make the pie and drag it somewhere out of the way. Select every brush of the pie, and then select the Slice tool. It's in the Modify menu.
Note that it is VERY IMPORTANT to only select brushes you intend to slice; as if nothing is selected, the tool will try to slice EVERY BRUSH IT REACHES.
Click anywhere on the selection to bring up an orange line. This is where the brushes will be sliced, so align it with the center hole. Once you have it sort of like this, hit the Make button.
Delete any unnecessary brushes... and that's one side done.
Repeat on all four sides; you'll have to adjust the Rotation field to get some of the sides, like so:
You'll get something that looks like this:
So we'll have to cut a square hole in our original brush. This is very easy and quite obvious to do, so I'll let you figure that out. It's still best not to take the lazy way out and CSG subtract.
Don't forget to actually drag your circle into the hole you just made.
Now you just work some texturing magic (see here for how to texture pie slices, aka just use Unify a lot) and...
Looks great, and is far more likely to convert than CSG subtracting.
Example map download: Here
Credit to Technostar for figuring this out ages ago, and credit to HiGuy for telling me how to do this in the first place.
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