A high resolution transmission electron microscopy study of multilayer films prepared by magnetron sputtering shows that the morphology of the growing interface in a-Si/Nb and a-SiN/NbN multilayers is remarkably uniform and smooth; this is in contrast to the polycrystalline AlN/NbN multilayers grown under similar conditions, which exhibit columnar grain structure with rough interfaces. For proper sputtering parameters, the amorphous layers seem to periodically restore a relatively smooth initial interface condition for the successive Nb (or NbN) layer growth, consequently interrupting the tendency toward increased roughness due to mechanisms such as columnar growth. Artificial multilayers having very flat interfaces could stimulate applications based on multilayer Josephson junctions.