Control of interfacial roughness and chemical mixing is critical in nanomaterials. For example, multilayers composed of ∼20 Å conductive layer sandwiched between two ∼50 Å ferromagnetic layers can exhibit giant magnetoresistance (GMR). This property has caused a tremendous recent increase in hard disk storage capacity, and can potentially result in a new generation of nonvolatile magnetic random access memories. It has been established that good GMR properties can be obtained when the interfacial roughness and interlayer mixing of these multilayers are low. However, flat interfaces in nanoscale multilayers are not thermodynamically stable, and cannot be obtained using thermal energy deposition processes such as molecular-beam epitaxy. Hyperthermal energy sputter deposition techniques using either plasma or ion-beam gun are able to create nonequilibrium flat interfaces, and have been shown to produce better GMR multilayers. In these processes, however, inert gas ions or neutrals with energies between 50 and 200 eV can impact the growth surface. This may be a major source for interlayer mixing. By using a molecular dynamics technique and a reduced order model, the composition profile across the thickness of multiply repeated Ni/Cu/Ni multilayers has been calculated as a function of the energy and the relative flux of the inert gas ions or neutrals as well as the layer thickness. The results indicate that the 50–200 eV inert gas impact caused atomic exchange between adjacent atomic layers near the surface. The probability of exchange increased with impact energy, but decreased with the number of overlayers. The exchange between Ni overlayer and Cu underlayer atoms was much more significant than that between Cu overlayer and Ni underlayer atoms. As a result, the Ni on Cu interfaces were much more diffuse than the Cu on Ni interfaces, in good agreement with experiments. At very high inert gas flux and impact energy, an increased probability for the underlying Cu atoms to be exchanged to the surface resulted in significant Cu surface segregation.