The model of indentation of a spherical punch with a rough surface into a thin elastic layer lying on an elastic half-space has been developed. A numerical-analytical solution is suggested based on the two-scales approach. At macroscale, the integral equation of the second kind is reduced to calculate the nominal contact characteristics, taking into account the surface layer thickness and its mechanical characteristics, as well as additional compliance due to surface roughness calculated from the microscale analysis. The influence of the punch roughness and the surface layer mechanical and geometrical characteristics on the nominal contact pressure distribution, on the nominal contact area and the indentation depth, as well as on the real contact area and pressures at the individual contact spots, is analyzed. The developed contact model can be used to analyze the indentation of the punch into the layered elastic base, taking into account the roughness of the punch surface, and can also be used to give a complete analysis of the roughness effect on the contact process at both scale levels. The results can be used to control the indentation of the rough-coated bodies.