This paper describes a simple set of patterning methods that are applicable to diverse substrates and allow the routine and rapid fabrication of protein patterns embedded within a background that consists of quasi-three-dimensional microstructures of a cell-resistant polymer. The ensemble of methods reported here utilizes three components to create topographically nonfouling polymeric structures that present cell-adhesive protein patterns in the regions between the microstructures: the first component is an amphiphilic comb polymer that is comprised of a methyl methacrylate backbone and pendant oligo(ethylene glycol) moieties along the side chain, physically deposited films of which are protein- and cell-resistant. ne second component of the fabrication methodology involves the use of different variants of soft lithography, such as microcontact printing to create nonfouling topographical features of the comb polymer that demarcate cell-adhesive regions of the third component: a cell-adhesive extracellular protein or peptide. The ensemble of methods reported in this paper was used to fabricate quasi-three-dimensional patterns that present topographical and biochemical cues on a variety of substrates, and was shown to successfully maintain cellular patterns for up to two months in serum-containing medium. We believe that this, and other such methods under development that allow independent and systematic control of chemistry, topography and substrate compliance will provide versatile "test-beds" for fundamental studies in cell biology as well as allow the discovery of rational design principles for the development of biomaterials and tissue-engineering scaffolds.