The work is devoted to the study of the processes of formation of multilayer nanostructures, their vacuum deposition, and the manufacture of a novel functional element of spintronics - superconducting spin valve, which is a multilayer structure consisting of ferromagnetic cobalt nanolayers separated by superconductor niobium films. Multilayer nanostructures are fabricated by magnetron sputtering on (111) silicon substrates at a temperature of 300K. The prototypes of the superconductingspin valve are prepared from multilayer nanostructures by the method of sharp focus reactive ion etching (FIB). Modeling was carried out using molecular dynamics methods.