Andrei,

Sure, with a circle tool (three types: one point radius from center, two points diameter, three points: 1 center 2 on edge) set tool option to 3D extrude (six types: 2D surface, 2D wall, 3D extrude, 3D converge, 3D wall, insert opening) and create a cylinder. Move cylinder through object (if you didn't create it in the right place to begin with) and boolean difference, pick object first then cylinder. This works for all objects regardless of surface type.

With planer surfaces (flat) just set one of the circle tools to the insert opening tool option (2 settings: through solid mass, through entire object).

Besides circles there are squares, rectangles, ellipses, and polygons with 3 to however many sides you want (can be changed dynamically) and drawn free form shapes.