Display omitted •STM lithography with silicon layers removal is realized on Si(1 0 0)-2×-Cl.•Voltage pulse leads to the formation of pits by removing one or two silicon layers.•The typical etched pit has a lateral size of 1–2 nm and a depth of 1–5 Å.•Pits can contain chlorine vacancies. We report the realization of STM-based lithography with silicon layers removal on the chlorinated Si(1 0 0)-2 × 1 surface at 77 K. In contrast to other STM lithography studies, we were able to remove locally both chlorine and silicon atoms. Most of the etched pits have a lateral size of 10–20 Å and a depth of 1–5 Å. In the pits in which the STM image with atomic resolution is obtained, the bottom is mainly covered with chlorine. Some pits contain chlorine vacancies. Mechanisms of STM-induced removal of silicon and chlorine atoms on Si(1 0 0)-2 × 1-Cl are discussed and compared with the well-studied case of STM-induced hydrogen desorption on Si(1 0 0)-2 × 1-H. The results open up new possibilities of the three-dimensional local etching with STM lithography.