This work explores a new technique for the out-of-plane patterning of metal thin films prefabricated on the surface of a polymer substrate. This technique is based on an ion-beam-induced material modification in the bulk of the polymer. Effects of subsurface and surface processes on the surface morphology have been studied for three polymer materials: poly(methyl methacrylate), polycarbonate, and polydimethylsiloxane, by using focused ion beam irradiation with He+, Ne+, and Ga+. Thin films of a Pt60Pd40 alloy and of pristine Au were used to compare the patterning of thin films with different microstructures. We show that the height of Pt60Pd40 thin films deposited onto poly(methyl methacrylate) and polycarbonate substrates can be patterned by He+ ion beams with ultrahigh precision (nanometers) while preserving in-plane features, at the nanoscale, of the pre-deposited films. Ion irradiation of the Au-coated samples results in delamination, bulging, and perforation of the Au film, which is attributed to the accumulation of gases from radiolysis at the film–substrate interface. The irradiation with Ne+ and Ga+ ions destroys the films and roughens the surface due to dominating sputtering processes. A very different behavior, resulting in the formation of complex, multiscale 3D patterns, is observed for polydimethylsiloxane samples. The roles of the metal film structure, elastic properties of the polymer substrate, and irradiation-induced mechanical strain in the patterning process are elaborated and discussed.