Different processes of nanostructure interactions and mechanisms of template and pore siltation were registered for different types of precipitated atoms. Single atoms, which reached the pore bottom, were observed for all types of precipitated atoms. The most complete and dense pore siltation was registered in the process of gallium epitaxy. The pore-filled with atoms can be considered as a quantum point and used to obtain optic and electric effects. When studying the siltation of coatings with pores of different dimensions with gallium atoms, it was found out that the number of atoms actively grows in the pore in the time interval of 20–120 pcs. The pore siltation after 120 pcs of condensation time is accompanied by the reconstruction of atomic structure that contributes to the stabilization of 134dependencies and slight decrease in the percentage of gallium atoms, which penetrated the pore.