We report on the orientation of nematic liquid crystals supported on highly regular, periodic, nanometer-scale structures formed from atomic steps on the surface of miscut silicon crystals thermally annealed in ultrahigh vacuum (UHV). Prior to removal from UHV, the silicon templates were passivated by reaction with methanol, acetone, or hydrogen and characterized by ultraviolet photoelectron spectroscopy using synchrotron radiation. In contrast to silicon substrates prepared in the past by wet chemical methods and substrates prepared by oblique deposition of metal and metal oxide films, the passivated templates prepared in UHV have highly regular single and bunched atomic steps that can be observed by scanning tunneling microscopy. Three independent measurements of the orientation of nematic liquid crystals of 4-cyano-4'-pentylbiphenyl (5CB) on these templates revealed the alignment of 5CB to be parallel to the atomic step edges on samples with periodic single atomic steps (similar to 0.3 nm height, similar to 15 nm width) as well as bunched atomic steps (similar to 5 nm height, similar to 70 nm width). Because the nanometer-scale structures of these surfaces are well-defined and readily manipulated on spatial scales comparable to the sizes of a range of biological species, these surfaces may be useful as templates for the detection of the binding of biological species through changes in the orientation of liquid crystals.