A method and an apparatus for smoothing surfaces on an atomic scale. The invention performs smoothing of surfaces by use of a low energy ion or neutral noble gas beam, which may be formed in an ion source or a remote plasma source. The smoothing process may comprise a post-deposition atomic smoothing step (e.g., an assist smoothing step) in a multilayer fabrication procedure. The invention utilizes combinations of relatively low particle energy (e.g., below the sputter threshold of the material) and near normal incidence angles, which achieve improved smoothing of a surface on an atomic scale with substantially no etching of the surface.