We experimentally compared the shapes and sizes of isolated domains created by the focused ion beam irradiation in the lithium niobate crystals doped by MgO with polar surface covered by dielectric (resist) layer and those with free surface. We attributed the larger sizes of isolated domains in the samples covered by the resist layer to ion localization in the resist. We revealed a change in the domain shape as a function of increasing dose and explained it in terms of kinetic approach taking into account the modification of the surface layers by ion irradiation. We applied the obtained knowledge for 1D and 2D periodical poling using ion beam. Finally, we created the 2D square 1-μm-period array of isolated domains with radius about 300 nm and maximal depth of all domains in the array up to 100 μm as well as the 1D pattern of through stripe domains with 2-μm-period in 1-mm-thick wafer.