The formation of the ferroelectric domain structure as a result of irradiation by focused ion beam of [100]-cut 0.61Pb (Mg1/3Nb2/3)O3-0.39PbTiO3 (PMN-PT) single crystals covered by surface artificial dielectric layer and with free surface was investigated. The dot irradiation resulted in formation of the wedge-like domains grown along [00-1] direction. For irradiation of the free surface, the domains are mainly located under the surface, while at the irradiated surface with an artificial dielectric layer the domains are located at the surface. It was shown that the subsurface wedge-shaped part of the domain is unstable and completely disappears after a month due to spontaneous backswitching under the action of the residual depolarization field. The revealed nonlinear dose dependence of the domain sizes was attributed to the distribution of the electric field using the point charge model. The domain interaction for the distance between irradiated dots below 30 μm has been revealed in all samples. It was shown that the decrease of the distance between irradiated dots in the created domain row leads to an increase in the length of the central domains, which is explained by the contribution of all injected charges to the switching field.