Understanding the mechanical properties of interphase regions in supported polymer thin films is critical as it yields key insights into the constitutive behavior of nanostructured materials. While studies have consistently shown that polymer layers near the substrate exhibit a stiffened response, the size of this region has been reported to vary based on the measurement approach, ranging from hundreds of nanometers in atomic force microscopy (AFM) nanoindentation experiments to a few nanometers in molecular simulations and thin film wrinkling experiments. Here we employ nanoindentation simulations using a coarse grained molecular dynamics approach to investigate the elastic moduli gradients near the substrate interface of a supported poly(methyl methacrylate) (PMMA) thin film. We find that indenter sizes commonly used in experiments give rise to observed interphase length scales that are larger than the regions in which polymer dynamics are significantly altered as quantified by the segmental molecular stiffness via the Debye-Waller factor (DWF) in simulations. We find that the measured interphase length xi(int) increases for larger indenter tip radii (R) and can be corroborated with the size dependence of the stress field following an R-1/2 scaling relationship. Accordingly, we show that extrapolation to vanishing R reproduces similar interphase lengths detected by the DWF. Our results elucidate possible origins of previous discrepancies in interphase measurements and suggest that the indenter tip radius and indentation depth are important factors that must be considered in measuring interphase properties with AFM.