This work is a study of the formation processes and the effect of related process parameters of multilayer nanosystems and devices for spintronics. The model system is a superconducting spin valve, which is a multilayer structure consisting of ferromagnetic cobalt nanolayers separated by niobium superconductor nanolayers. The aim was to study the influence of the main technological parameters including temperature, concentration and spatial distribution of deposited atoms over the nanosystem surface on the atomic structure and morphology of the nanosystem. The studies were carried out using the molecular dynamics method using the many-particle potential of the modified embedded-atom method. In the calculation process the temperature was controlled using the Nose–Hoover thermostat. The simulation of the atomic nanolayer formation was performed by alternating the directional deposition of different composition layers under high vacuum and stationary temperature conditions. The structure and thickness of the formed nanolayers and the distribution of elements at their interfaces were studied. The alternating layers of the formed nanosystem and their interfaces are shown to have significantly different atomic structures depending on the main parameters of the deposition process.