Deposition of a plasma polymerized film on a silicon substrate substantially changes the fluctuations on the surface of a sufficiently thin melt polystyrene (PS) film atop the substrate. Surface fluctuation relaxation times measured with X-ray photon correlation spectroscopy (XPCS) for ca. 4Rg thick melt films of 131 kg/mol linear PS on hydrogen-passivated silicon (H-Si) and on a plasma polymer modified silicon wafer can both be described using a hydrodynamic continuum theory (HCT) that assumes the film is characterized throughout its depth by the bulk viscosity. However, when the film thickness is reduced to ∼3Rg, confinement effects are evident. The surface fluctuations are slower than predicted using the HCT, and the confinement effect for the PS on H-Si is larger than that for the PS on the plasma polymerized film. This deviation is due to a difference in the thicknesses of the strongly adsorbed layers at the substrate which are impacted by the substrate surface energy.