The oxidation of a hydrogen terminated Si surface can locally be induced with a scanning tunnelling microscope (STM) operating in air or with a beam of free electrons in a controlled oxygen environment. The oxidation mechanism of both processes was studied and compared. The oxidation with the STM in air depends strongly on the applied tip‐substrate voltage and writing speed, but is not proportional to the tunnelling current. This is in contrast to the process with a beam of free electrons. The thickness of the electron beam induced oxide is studied as a function of electron energy, electron dose, and oxygen pressure. Oxide thicknesses of 0.5–3 nm are measured using Auger spectroscopy. The initial step of the oxidation process is the electron beam induced removal of hydrogen from the surface. The electron dose requirement for this step was determined as a function of electron energy. The dose is found to be minimal for 100 eV electrons, and is ≊4 mC/cm2. Oxide lines made with the STM on Si(110) were used as a mask to wet etch the pattern into the Si(110). With tetramethyl ammonium hydroxide, a selective anisotropic etch liquid, trenches with a width of 35 nm and a depth of 300 nm were made. We show that it is also possible to locally oxidize hydrogenated amorphous silicon (a‐Si:H) and use the oxide as an etching mask. Hydrogenated amorphous silicon has the advantage that it can be deposited in very thin layers on almost any substrate and therefore has great potential as STM and electron‐beam resist.