This study sought to fabricate a three-dimensional structure on a silicon surface using a combination of tribo-nanolithography (TNL) and wet chemical etching. TNL forms an amorphous phase on a single-crystal silicon surface that has an etch resistance against potassium hydroxide (KOH). A protruding structure can then fabricated with wet chemical etching. When the machined silicon is etched in hydrofluoric acid (HF), the amorphous silicon phase formed by the TNL is selectively etched whereas the non-machined silicon withstands the etching. The etch resistance of the TNL-induced amorphous phase can be controlled by the machining conditions, such as the normal load, overlap ratio, and number of times the area is machined. In this study, the resulting mechanism controlling the etch resistance was examined under different machining conditions. Changes in the etch resistance due to the normal load were caused by the thickness of the amorphous phase, while changes in the resistance due to the overlap ratio or number of times the area was machined were caused by the density of the amorphous phase.