In this work, we study the behavior of a thin gold layer on the surface of a polymethyl methacrylate (PMMA) film under irradiation with keV atomic P and molecular PF4 ions. Transformation of both the gold layer and the PMMA film depends on the kind of ions used. Formation of gold nanoparticles is found in all cases. This process is less efficient than in the case of the ion-beam-induced Au layer dewetting on SiO2 substrate. The formation of nanostructured regions in the polymer bulk was also established. The dependence of transmission in the IR range on the stage of formation of nanostructures has been investigated. The PMMA matrix destruction is low as revealed by FTIR investigation. Obtained structures could be used as efficient substrates for surface enhanced Raman scattering studies.