Subtract (difference)

Cut later shapes out of the first.

Subtract cuts every other selected shape out of the first one you selected — the way you carve holes and pockets.

Selection order is what decides which solid is kept, so if the cutter won and your model vanished, the two were picked the other way round. That is easy to do and easy to undo: select the Subtract in the scene tree and press Flip order in the Properties panel, which swaps which shape is kept and which is removed without rebuilding anything. The Properties panel also spells the current order out in words, so you can read it before you commit.

A subtract that removes everything looks exactly like a subtract that did nothing — the whole model disappears either way. If that happens, reach for Flip order before assuming the tool failed.

With three or more shapes, Flip order reverses the whole list, which is blunt when you only want a different one kept. Right-click any shape inside the Subtract in the scene tree and use Move up / Move down — or Alt+↑ / Alt+↓ with the row focused — to move just that one. Whichever shape ends up first is the one that survives.

1. Select shapes; the first one you picked stays, the rest cut into it.
2. Open Combine → Subtract.
3. The overlap is removed.
4. Wrong way round? Select the result and press Flip order in the Properties panel.
5. Three or more shapes? Right-click any one in the scene tree and use Move up / Move down (Alt+arrow).