In polymer nanocomposites (PNCs), the physical and chemical interactions at the polymer matrix-filler interface lead to local variations in polymer properties over a substantial "interphase" region in the vicinity of the interface. Characterization of mechanical properties in the polymer interphase region is essential for informed modeling and design of advanced PNCs. Direct contact measurement of the mechanical properties in the interphase region has been performed via high-resolution scanning probe nanoindentation experiments on model polymer-substrate samples. However, the force-displacement data from indentation experiments are affected by the interaction of the elastic stress field with the substrate, which limits determination of the interphase properties close to the polymer-substrate boundary. To extract the mechanical properties of the interphase from experimentally measured data, three-dimensional finite element analysis (3D FEA) models are developed in this study to simulate the indentation experiments on model nanocomposites samples. The simulation results quantify the substrate effects and allow them to be excluded from experimental data analysis. The results also provide insight into the role of tip deformation and tip radius during the measurement of the modulus profile of the interphase.