Extruded faces from cylinder not being treated properly in Boolean

The setup is pretty simple. I start with 1 cube, two cylinders:

• Create a thick rectangle (Shift+A > Mesh > Cube > size to fit)
• Create a cylinder (Shift+A > Mesh> Cylinder > size to fit)
• Copy first cylinder mesh (Right click first cylinder > Duplicate object > move laterally)

In top view (Numpad 7), delete half of the second cylinder, leaving an array of faces. I then select all faces of the half-cylinder and extrude them (Tab for Edit mode > Delete half of the vertices on top and bottom, leaving a semi-circular face, A to select, E to extrude)

After exiting Edit mode, I drag both objects down through the surface of the cube. Using the "Boolean" modifier twice, I first find the difference between: (1) Right cylinder and cube, and (2) left..half..cylinder thing and cube, pressing Ctrl+A after each operation to execute the modifier:

The modifier clearly works with the unmodified (right) cylinder, while it does not work with the modified (left) cylinder. However, something is happening, because the top surface of the cube shows the outline of the modified (left) cylinder. Furthermore, if I zoom "into" the cube to look around the inside, there are no other faces there. I've tried right-clicking the modified cylinder and converting to a Mesh, but this still doesn't work.

What am I not seeing? How can I fix this?

• Recalculate the normals on both cutters. It sounds as if one of them has inverted normals which can happen when extruding. You can check by turning on the Face Orientation overlay in the Viewport Overlays menu. Red means inverted, Blue is ok. In Edit mode on the red object, select All then use Shift-N to recalculate the normals. See my answer here. Mar 14 at 22:22
• Thanks! This is exactly what I needed, resolved my issue. Mar 14 at 23:15
• Good! That seems to be quite a common problem with Booleans especially when the cutter has been shaped by extruding. Mar 14 at 23:35
• The default cylinder has its faces oriented like you would suppose, pointing their outside outwards and their inside inwards. When you delete half of the cylinder and extrude it towards where the inside was, you extrude the faces to the opposite side of their normals and thus inverting them, so that the the object is now flipped inside out. While extruding you will see the amount or distance how far you extrude (let's assume e.g. 1.5 m) showing "D: -1.5 m (1.5 m) normal". The minus sign indicates that you are in this moment flipping the normals. Mar 16 at 10:50