Using Grazing-incidence small-angle scattering (GISAXS) technique we investigated the surface morphology of polymer films spin-coated on different silicon substrates. As substrates we used either technologically smooth silicon wafers or the same silicon wafer coated with thin aluminium or gold films which show a granular structure at the surface. Although the polymer thickness exceeds 300nm the GISAXS pattern of the film shows the same in-plane angle distribution Δ2Θ as the underlying substrate. Annealing the polymer films at a temperature above its glass transition temperature Δ2Θ changed from a broad to a narrow distribution as it is typically for films on pure silicon. The experiment can be interpreted by roughness replication and density fluctuation within the polymer film created while spin-coating at room temperature. Due to the low segment mobility there are density fluctuations which repeat the surface morphology of the substrate. Above the glass temperature the polymer density can be homogenized independently from the morphology of the substrate.