C4D Knife Tool 008 - Delete Original Polys


You should have Cube.1 in the list now - rename it to Cube.1 Windows (or anything) by double clicking so you don't lose it.
Next > Select the original Cube in the Objects list


With Cube selected use the main menu Edit > Delete.
If you use the Backspace or Delete key the whole Cube will evaporate and dissappear.
This behavior may have been 'fixed' in version 9. I only know the way described above is what works in 8.5.