A scanning tunneling microscope (STM) was used to investigate tip-induced chlorine desorption and lithographic patterning of Cl-terminated Si(100)-(2 x 1) surfaces from 4 to 600 K in ultrahigh vacuum. Until now, STM lithography has exclusively focused on hydrogen-based chemistry for donor device fabrication. As the initial step in developing halogen-based chemistries for STM fabrication of acceptor-based devices, we substituted the hydrogen resist with chlorine. We found that chlorine can be selectively desorbed by the STM tip using both electron and hole injection. Observations show that targeted chlorine was not driven into the surface but desorbed completely as both individual and pairs of atoms. Chlorine depassivation lithography is demonstrated using both field-emission patterning to desorb chlorine from large areas with high efficiency (0.83(1)) and atomic-precision patterning to desorb one to two dimer rows at a time, resulting in 1.5 nm wide lines. Further, varying the experimental parameters for lithography revealed a positive correlation between pattern line widths and both positive sample bias voltage (1.7(2) nm/V) and total electron dose (0.15(2) nm/(mC/cm)), demonstrating that the energy and total number of electrons play a role in desorption from multiple sites.