As a maskless nanofabrication technique, friction-induced selective etching can easily produce nanopatterns on a Si(100) surface. Experimental results indicated that the height of the nanopatterns increased with the KOH etching time, while their width increased with the scratching load. It has also found that a contact pressure of 6.3 GPa is enough to fabricate a mask layer on the Si(100) surface. To understand the mechanism involved, the cross-sectional microstructure of a scratched area was examined, and the mask ability of the tip-disturbed silicon layer was studied. Transmission electron microscope observation and scanning Auger nanoprobe analysis suggested that the scratched area was covered by a thin superficial oxidation layer followed by a thick distorted (amorphous and deformed) layer in the subsurface. After the surface oxidation layer was removed by HF etching, the residual amorphous and deformed silicon layer on the scratched area can still serve as an etching mask in KOH solution. The results may help to develop a low-destructive, low-cost, and flexible nanofabrication technique suitable for machining of micro-mold and prototype fabrication in micro-systems.