The extracellular matrix (ECM) is a complex, spatially inhomogeneous environment that is host to myriad cell-receptor interactions that promote changes in cell behavior. These biological systems can be probed and simulated with engineered surfaces, but doing so demands careful control over the arrangement of ligands. Here, we describe how such surfaces can be fabricated by utilizing polymer pen lithography (PPL), which is a cantilever-free scanning probe lithographic method that utilizes polymeric pen arrays to generate patterns over large areas. With the advent of PPL, fundamental questions in cell biology can be answered by recapitulating cell-ECM interactions to explore how these interactions lead to changes in cell behavior. Here, we describe an approach for the combinatorial screening of cell adhesion behavior to gain understanding of how ECM protein feature size dictates osteogenic differentiation of mesenchymal stem cells. The technique outlined here is generalizable to other biological systems and can be paired with quantitative analytical methods to probe important processes such as cell polarization, proliferation, signaling, and differentiation.