Low energy ion polishing is attractive in thin films because of the small interaction zone with the treated material. In this context, various noble gases (Ne, Ar, Kr, and Xe) have been applied for low energy ion polishing of interfaces in nanoscale optical Mo/Si multilayers in order to mitigate the evolving roughness during the deposition process. The interface morphology has been studied by grazing incidence small angle x-ray scattering, the multilayer composition by x-ray photoelectron spectroscopy, and the general performance by extreme ultraviolet (EUV) reflectometry. Both the average roughness level and the vertical correlation length of the roughness can be reduced significantly by increasing the atomic mass of the ion species applied for polishing. Maximum EUV reflectance is observed for Krþ-polishing, while Xeþ-polishing shows a superior structure. This apparent contradiction is explained by taking into account the optical absorption from noble gas residuals in the amorphous silicon layers.