Hexagonally patterned lysozyme nanoarrays have been assembled on silicon wafers by combining nanosphere lithography and surface silane chemistry using vapor and solution deposition processes. The patterned protein regions extend over cm sized regions, and the size of each island is similar to 120 nm for the solution-prepared template and similar to 60 nm for the vapor-prepared template. Antibody test indicates that the patterned lysozyme maintains its bioactivity on the surface. This new approach offers a fast and reliable method to fabricate protein arrays over large areas with feature sizes comparable to scanning-probe based techniques.