Methods and systems for direct lithographic pattern definition based upon electron beam induced alteration of the surface chemistry of a substrate are described. The methods involve an initial chemical treatment for global definition of a specified surface chemistry (SC). Electron beam induced surface reactions between a gaseous precursor and the surface are then used to locally alter the SC. High resolution patterning of stable, specified surface chemistries upon a substrate can thus be achieved. The defined patterns can then be utilized for selective material deposition via methods which exploit the specificity of certain SC combinations or by differences in surface energy. It is possible to perform all steps in-situ without breaking vacuum.