In order to explore whether low-energy ion bombardment of island thin films can be applied for preparation of nanoparticles supported on solid surfaces, morphological and compositional modifications of discontinuous silver layers deposited onto amorphous carbon or native oxide covered silicon substrates were followed by transmission electron microscopy (TEM) and electron spectroscopy during sputter etching with Ar+ ions. TEM micrographs confirmed the formation of isolated nanoparticles, while electron spectroscopic measurements supported the lack of chemical interaction and appreciable intermixing, although the latter is considered to be a major drawback of the method. Comparative studies carried out on the gold/silicon system with a strong tendency towards spontaneous alloying revealed that the unavoidable mixing due to ballistic effects can be compensated by chemically guided diffusion processes governed by the thermodynamic properties of the film/substrate pair. According to the theoretical description of ion-induced mixing, such a mechanism is feasible if the components of the film/substrate pair tend to segregate in equilibrium, which gives the necessary condition for the success of ion etching induced nanoparticle preparation.