A method for processing a silicon substrate includes forming a structure having a bottom surface and a depth of 200 μm or more or 300 μm or more from a first surface of a silicon substrate, forming a protective film on an inner wall of the structure, and performing plasma etching so as to selectively remove the protective film disposed on the bottom surface of the structure with respect to the protective film disposed on the substantially perpendicular side wall of the structure, wherein the plasma etching is performed under the condition in which plasma with a sheath length at least 10 times the depth when the depth is 200 μm or more, or at least 5 time the depth when the depth is 300 μm or more, is generated and a mean free path of ions generated in the plasma is longer than the sheath length.