Micropatterns of different biomaterials with micro- and nanoscale features and defined spatial arrangement on a single substrate are useful tools for studying cellular-level interactions, and recent reports have highlighted the strong influence of scaffold compliance in determining cell behavior. In this paper, a simple yet versatile and precise patterning technique for the fabrication of interdigitated micropattems of nanocomposite multilayer coatings on a single substrate is demonstrated through a combination of lithography and layer-by-layer (LbL) assembly processes, termed polymer surface micromachining (PSM). The first nanofilm pattern is constructed using lithography, followed by LbL multilayer assembly and lift-off, and the process is repeated with optical alignment to obtain interdigitated patterns on the same substrate. Thus, the method is analogous to surface micromachining, except that the deposition materials are polymers and biological materials that are used to produce multilayer nanocomposite structures. A key feature of the multilayers is the capability to tune properties such as stiffness by appropriate selection of materials, deposition conditions, and postdeposition treatments. Two- and four-component systems on glass coverslips are presented to demonstrate the versatility of the approach to construct precisely defined, homogeneous nanofilm patterns. In addition, an example of a complex system used as a testbed for in vitro cell adhesion and growth is provided: micropatterns of poly(sodium 4-styrenesulfonate)/poly-L-lysine hydrobromide (PSS/PLL) and secreted phospholipase A(2)/poly(ethyleneimine) (sPLA(2)/PEI) multilayers. The interdigitated square nanofilm array patterns were obtained on a single coverslip with poly(diallyldimethyl ammonium chloride) (PDDA) as a cell-repellent background. Cell culture experiments show that cortical neurons respond and bind specifically to the sPLA(2) micropatterns ill competition with PLL micropatterns. The fabrication and the initial biological results on the nanofilm micropattems support the usefulness of this technique for use in studies aimed at elucidating important biological structure-function relationships, but the applicability of the fabrication method is much broader and may impact electronics, photonics, and chemical microsystems.