Fabrication of spatially well-defined, ordered bacterial S-layer arrays of the protein SbpA of Bacillus sphaericus CCM 2177 at silicon supports is achieved by exploiting the soft lithography technique, micromolding in capillaries, as a nonlithographic patterning tool. Lateral patterning of simple and moderately complex crystalline S-layer array structures ranging in critical dimension from submicron to hundreds of microns is demonstrated. For micron-scale patterned S-layers, the integrity of the native chemical functionality of the protein following patterning is verified by covalent attachment of human IgG antibody and subsequent binding of antihuman IgG antigen. The structural diversity of S-layers combined with their ease of patterning, self-assembly, and surface chemical modification suggest that this approach could be exploited for biomimetic fabrication of a wide range of functional nanostructures.