The method of modification of the surface structure of the systems thin metal film -thick lithium niobate substrate is proposed. The ion implantation as a part of the technology process must be carried out by Ar+ ions with optimal energies and dozes. Depending of the film material, structure changes may be different: from little bubbles for Ni film to large craters and holes in the system for Pd film. The surface structure of such systems was researched by electron microscopy and Atomic Force Microscopy. The X-ray investigations of implanted systems are carried out too. The distinctions in the structure of implanted and nonimplanted systems are found. The theoretical calculations of profiles of braking recoil atoms are carried out by Monte-Carlo method for the energies of Ar+ ions of 50, 100 and 150 keV. It is found that the greatest degree of an amorphyzation in such systems is observed on depth conforming to a maximum of distribution of recoil atoms. It is shown that the considerable changes of the structure of the researched systems do not result in sufficient changes of optical properties of these systems owing to an implantation. The implanted systems thin metal film -thick lithium niobate substrate is proposed for effective using in modern opto-electronic devices with improved optical characteristics.