We have investigated the influence of swift heavy ion (SHI) irradiation as well as thermal annealing on the interface roughness in thermally immiscible Fe/Au and Fe/Ag multilayers. The 5-fold multilayers consisted of 20–25nm Fe-, 10nm Ag- and 7–21nm Au-layers and were partly irradiated at liquid nitrogen temperature with 80–350MeV Ar, Ni, Kr, Xe ions at fluences between 1012cm−2 and 1015cm−2. The irradiated as well as the unirradiated parts of the samples were analyzed by means of Rutherford backscattering spectrometry (RBS) using 1MeV He+ ions. In the case of Fe/Ag, no change in the RBS spectra due to the ion irradiation could be detected, while in the case of Fe/Au, a clear increase of the steepness of the high energy edge of the Au signal was observed. A detailed analysis of the RBS Au profiles in comparison with RBS simulations for different shapes of the Au-layers allowed us to conclude that SHI irradiation results in smoothing of the Fe–Au interfaces, which can be understood in terms of a local minimization of the interface energy. In the Fe/Ag case, the symmetry of the RBS profiles of the Ag layers indicated that the interfaces became already smooth during the layer deposition. Heating of the Fe/Au multilayers resulted in broadening of the Au profiles and finally a complete destruction of the multilayer structure was observed. Here the whole sample is at high temperature and therefore interface energy minimization now occurs by the formation of spherical Au particles, which destroys the layered structure.