The formation of the domain structure created by the focused electron beam in lithium niobate crystals with waveguides was studied. Formation of domains of arbitrary shape as a result of discrete switching was revealed. Dependences of the morphology and size of the domain structure on the irradiation parameters were measured. For the first time, periodical domain structure has been created in channel waveguides created by the proton exchange method. Second harmonic generation has been obtained with conversion efficiency at the level of the best world achievements.