Polydimethylsiloxane (PDMS) is a bioinert synthetic polymer with tunable elastic properties that is commonly used as a cell culture substrate. Although plasma treatments are widely used to bio-functionalize otherwise hydrophobic PDMS surfaces, plasma altered surface mechanical properties and implications for cell–substrate mechanical interactions are poorly understood. We performed a multi-scale mechanical characterization of PDMS following plasma treatment: spherical indentation tests were performed with a universal testing machine (indenter diameter, d = 4.75 mm) and atomic force microscopy (AFM) with round tips of 2 different diameters (d = 2 μm, d = 20 μm). Results indicated substantial surface stiffening at indentation depths up to 1 micron, with exponentially decreasing effects to depths of 1 mm. AFM indentation results were analyzed using a finite element (FE) based optimization to determine the substrate material properties, and thus separate the confounding influence of the underlying substrate on surface indentation experiments. We found that a two-layer material model composed of a thin, stiff plasma-oxidized layer (296 nm and 3.66 MPa, respectively) superimposed on a thick layer of bulk polymer (elastic modulus of 10.5 kPa) was able to robustly fit the experimental data. We then investigated the repercussions of the biopolymer surface modifications on cell mechanics, using an inverse finite element model to interpret cell–matrix force exchange. Estimates of cell elastic modulus neglecting the mechanical effects of plasma treatment were more than an order of magnitude lower than estimates accounting for the surface layer (9.6 ± 4.2 kPa vs. 124 ± 55 kPa, respectively). This study thus highlights the need to accurately consider biomaterial surface modifications and how they may influence cell–biomaterial interaction. It further provides a novel approach to characterizing cell-relevant mechanical properties of a polymer substrate. These advances may lead to an improved quantitative assessment of actin cytoskeleton function, with potential relevance to biomaterial based therapies.