The formation of the periodic structures based on Si-materials by electron beam lithography technique has been studied. We have investigated lithography processes such as designing, exposition, development, etching end others. The developed technique allows forming close-packed arrays of elements and holes in the nanometre range. This can be used to produce two-dimensional photonic crystals (2D PhCs) with emitting micro cavities (missing holes) with lateral size parameters within an accuracy of about 2% in the Si (100) substrate and in silicon-on-insulator structures. Such accuracy is expected to be sufficient for obtaining the cavities-coupling radiation interference from large areas of 2D PhCs.