The formation of morphological structures on system SiO2/Si by pulsed ytterbium fiber laser has been investigated. The resulting structures are investigated by atomic force microscopy. It is shown that during irradiation on surface of the monocrystalline silicon wafer covered by a thin layer of thermally grown silicon dioxide (SiO2), there are significant structural changes associated with localization on the surface of the silicon strips of slip-lines and grid of slip-line formed by the intersection of these strips. It is also shown that exposed to laser radiation in the silicon-silicon dioxide system there are structural changes that lead to the change of the electrophysical properties of SiO2/Si system. Changes in electrophysical properties of the oxide and the interface are more observed in the area of direct exposure to the laser beam on the silicon substrate where there are maximum structural changes of the silicon surface manifested in the form of a lattice slip lines. It is found that there are laser-induced defects in areas remote from the irradiation zone.