We introduce here our last results on the ultra high vacuum scanning tunneling microscope study of the initial formation of thin films deposited by low energy ion beam on HOPG. Defects of different nature may appear as similar perturbations of the electronic partial density on STM high resolution images. By analyzing the symmetry of perturbation patterns we were able to identify several categories of defects and particularly discriminate between adsorbed atoms, single and multiple vacancies and interstitial. For the purpose of comparison of their influence on the formation of nano-islands, films were grown by two methods: first by using low energy ions of carbon and nickel at high density (up to 50 ions/nm(2)), and second, by using molecular jets of nickel and other metals. In particular, we investigate the role of defects induced by ions on the size, density and structure of islands. We reveal several modes of coalescence in the Stranski-Krastanov class of growth. Finally, we show how low energy ion beams enable the control of size, density and structure of self-assembled nanoparticles on a substrate.