The mechanical properties of polymeric nanocomposites are strongly affected by the nature of the interphase between filler and matrix, which can be controlled by means of surface chemistry. In this report, we utilize intermodulation atomic force microscopy (ImAFM) to probe local mechanical response with nanometer-scale resolution of poly(dimethylsiloxane) (PDMS) coatings with and without 20 wt% of hydrophobic silica nanoparticles. The data evaluation is carried out without inferring any contact mechanics model, and is thus model-independent. ImAFM imaging reveals a small but readily measurable inhomogeneous mechanical response of the pure PDMS surface layer. The analysis of energy dissipation measured with ImAFM showed a lowering of the viscous response due to the presence of the hydrophobic silica nanoparticles in the polymer matrix. An enhanced elastic response was also evident from the in-phase stiffness of the matrix, which was found to increase by a factor of 1.5 in presence of the nanoparticles. Analysis of dissipation energy and stiffness in the immediate vicinity of the nanoparticles provides an estimate of the interphase thickness. Because the local stiffness varies significantly near the nanoparticle, AFM height images contain artifacts that must be corrected in order to reveal the true surface topography. Without such a correction the AFM height images erroneously show that the stiff particles protrude from the surface, whereas corrected images show that they are actually embedded in the matrix and likely covered with a thin layer of polymer.