In recent experiments we have patterned smooth HOPG surfaces with periodic arrays of nanometer dimension holes on a 20nm lattice using two-dimensional (2-D) protein crystals as templates. The bacterial cell wall crystals were deposited on HOPG substrate and overcoated at oblique incidence with an ultrathin (3.5 nmn) TiO2 film. Fast atom beam (FAB) milling patterns the TiO2 film into a screen having the protein lattice periodicity and the screen then acts as a mask for the pattern transfer to the HOPG substrate. This method provides an inexpensive, “benchtop,” intrinsically parallel technique for the periodic nanostructuring of surfaces. Here we extend it to the patterning of silicon single crystal surfaces. We will describe the use of silane coupling agents to enable protein adhesion with the cytoplasmic side up, as is preferable for the patterning. We will show AFM images of the T1O2 -protein-silicon composite surface at various stages of the fabrication process.