A process for area selective atomic layer deposition (ALD) at the near atomic scale (sub 10 nm) is disclosed. A substrate surface is cleaned and terminated with hydrogen and a pattern written in the hydrogen terminated surface by selectively depassivating the surface using scanning tunneling microscope lithography. The depassivated regions are subjected to a halogen flux with the thus passivated regions further subjected to a functionalization process creating functionalized regions. The role of hydrogen and halogen can be inverted to invert the tone of the pattern. The substrate is then subjected to the ALD process, with growth occurring only in the non-functionalized regions. The substrate may then optionally be subjected to selective etching to remove the functionalized regions and the portions of the substrate under the functionalized regions.