Nanoscale patterning of the Si(100)‐2×1 monohydride surface has been achieved by using an ultrahigh vacuum (UHV) scanning tunneling microscope(STM) to selectively desorb the hydrogen passivation. Hydrogen passivation on silicon represents one of the simplest possible resist systems for nanolithography experiments. After preparing high quality H‐passivated surfaces in the UHV chamber, patterning is achieved by operating the STM in field emission. The field emitted electrons stimulate the desorption of molecular hydrogen, restoring clean Si(100)‐2×1 in the patterned area. This depassivation mechanism seems to be related to the electron kinetic energy for patterning at higher voltages and the electron current for low voltage patterning. The patterned linewidth varies linearly with the applied tip bias achieving a minimum of <10 Å at −4.5 V. The dependence of linewidth on electron dose is also studied. For positive tip biases up to 10 V no patterning occurs. The restoration of clean Si(100)‐2×1 is suggestive of selective area chemical modifications. This possibility has been explored by exposing the patternedsurface to oxygen and ammonia. For the oxygen case, initial oxidation of the patterned area is observed. Ammonia dosing, on the other hand, repassivates the surface in a manner different from that of atomic hydrogen. In both cases the pattern resolution is retained and the surrounding H‐passivated areas remain unaffected by the dosing.