Nanostencils (shadow masks with submicrometer apertures in a thin silicon nitride membrane) are promising tools for the facile one-step generation of nanopatterns of various materials by physical vapor deposition. Evaporation through a shadow mask is accompanied by gradual clogging of the apertures due to adhesion of evaporated material. In order to reduce this effect, nanostencils were coated with alkyl and perfluoroalkyl self-assembled monolayers (SAMs). The formation and properties of SAMs on planar silicon nitride substrates were studied by contact angle goniometry, X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM). The SAMs are stable under evaporation of gold at various angles. SAM-coated nanostencils showed considerably less adhesion of gold compared to bare SixNy stencils.