Metallic superlattices with planar, unalloyed (unmixed) interfacial structures are difficult to fabricate by all conventional vapor deposition methods. Molecular dynamics simulations have been used to explore the ways in which inert gas ions can be used to control the atomic assembly of a model Cu/Co metallic super lattice system. High energy, high atomic weight ions are shown to smooth rough interfaces but introduce undesirable intermixing at interfaces. Light ions with very low energies fail to flatten the rough surfaces that are naturally created during deposition at ambient temperature where surface atom mobility is kinetically constrained. The optimum energies for achieving the lowest combination of interfacial roughness and interlayer mixing have been found for each inert gas ion species and the key mechanisms of surface structure reorganization activated by ion impacts have been identified over the range of ion masses and energies studied. Optimum ion energies that maximize the interface structural perfection have been identified.