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I have this object here that has a boolean modifier on the Cube with a sphere as the cutout object.

box

but when I export to STL, the stl looks like that

stl

I checked Apply Modifiers on export but the cut out does not work. Is there something else I am missing? Do I have to merge those two object to be able to export to stl?

Just joined the objects and saw that the joined object does look like the STL version. So somehow the boolean does not seem to work right on joining, gotta Google that.

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Ok, I found the solution. Turns out you can hit Apply on the Boolean modifier to actually apply the effect. Then the modifier is gone and the vertices are created in the cube object. You can do that by hitting this button in the modifier tab:

apply

After exporting the STL looks like expected, great

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