OpenSCAD Tutorial

To cut a hole, subtract a cylinder. If the cylinder were exactly as tall as the plate, its top and bottom faces would sit exactly on the plate's faces. Preview can then show a flickering paper-thin skin over the hole, and the result is ambiguous.

The eps trick fixes that: start the cutter a tiny eps below the bottom and make it 2 * eps taller, so it passes all the way through.

translate([x, y, -eps])
  cylinder(h = thickness + 2 * eps, d = 8, $fn = 48);

See how to cut holes in OpenSCAD for blind holes and countersinks.

Your task: cut a 12 mm hole through the center of the 40 × 25 × 5 plate, using the eps trick.