Fabrication of multicomponent patterned films comprising polymer/nanoparticle multilayers using conventional lithography and bottom-up layer-by-layer nanofabrication techniques is described. The work is motivated by the potential to extend polymer surface micromachining capabilities toward construction of integrated systems by connecting discrete domains of active materials containing functional nanoparticles. Modified surfaces illustrate tunability of the physical (thickness, roughness, 3D structures) and chemical (inorganic/organic material combinations) properties of the nanocomposite micropatterns. Intriguing nanoscale phenomena were observed for the structures when the order of material deposition was changed; the final multilayer thickness and surface roughness and mechanical integrity of the patterns were found to be interdependent and related to the roughness of layers deposited earlier in the process.