In present work the application of ion scattering, sputtering and implantation processes for study of surface structure and for its modification has been investigated by computer simulation. The geometry and composition of structured materials may be determine by small angle ion scattering. The ion implantation and preferential sputtering lead to change of a profile of composition and structure of thin layers on the surface. At grazing incidence the ions of primary beam penetrate in several nearest to surface atomic layers during the process of their movement in channels of low index directions along surface. As a result of partial sputtering of surface atoms and implantation of primary ions the structure of surface layers is changed in nanoscale. It was shown that by the data of scattered particles, one may determine a presence and a spatial extension of the isolated atomic steps on the single crystal surface. The sputtering yields of one- and multicomponent crystals versus the grazing angle of incidence have been calculated. It was shown that in this case the layer-by-layer sputtering is possible and its optimum are observed within the small angle range of the glancing angles near the threshold sputtering angle. The depth distributions of 5 keV Ar ions implanted into Cu(001) surface and 1 keV Be and Se ions implanted into GaAs(001) have been calculated. It was shown that at grazing incidence the main peak of the implanted depth distributions is considerably shallower than that for large angles of incidence. The range for Se is shallower and the half-width of profile for Se is narrow than that for Be. These results allow to select the optimum for obtaining implanted depth distributions with demanded shape in narrow near-surface area.