This paper presents the results of experimental studies of the modes of formation of nanosized structures on the surface of a silicon substrate by the method of focused ion beams (FIB). The regularities of the effect of the ion beam current, accelerating voltage, and radiation dose on the surface morphology of nanoscale structures are determined. The modes under which the effects of implantation swelling (structure height up to 3 nm) and etching (structure depth up to 8 nm) manifest themselves are determined. The average roughness of the resulting structures varies from 0.13 to 0.24 nm. The results can be used in the development of technology for manufacturing instrument structures in nanoelectronics and nanophotonics.