Vacuum environments provide capabilities for patterning molecularly thin films that are air sensitive, insoluble, or cannot be easily dissolved in solvents. The authors introduce an approach to produce nanopatterns with organotrichlorosilanes using vacuum-line deposition combined with colloidal lithography. In particular, excess water can be problematic for preparing films of organosilanes due to self-polymerization. Three model trichlorosilane architectures were tested: octadecyltrichlorosilane, 4-(chloromethyl)phenyltrichlorosilane (CMPS), and phenyltrichlorosilane. Monodisperse silica mesospheres were used as a surface mask to protect exquisitely small, discrete areas of a silicon surface from reaction with organosilanes. Organosilanes were deposited with a home-built vacuum-line apparatus to form patterns on Si(111) surrounding the surface template of close-packed silica spheres. After removing the mask by solvent rinses, an array of nanoholes within a monolayer film of organosiloxanes was produced. Broad areas of the sample were patterned with regular arrangements of nanoholes, spanning microns. The thickness of the films was measured locally with atomic force microscopy by referencing the exposed sites inside the nanoholes as a baseline. As a comparison, nanostructures of CMPS were prepared at atmospheric pressure with conditions of ambient humidity. The nanostructures that were prepared in ambient pressure without control of even small amounts of residual water on the surface were comprised of cross-linked multilayers to form bowls surrounding the templating spheres of the surface mask. The nanostructured surfaces have precisely regular, reproducible geometries with nanoscale dimensions, which can subsequently furnish a template for successive chemical reactions.