The fabrication of the periodic structures, that is two-dimensional photonic crystals (2D PhCs) based on Si-materials by electron beam lithography (EBL) technique has been studied. We have investigated basic lithography processes such as designing, exposition, development, etching and others. The developed top-down approach allows close-packed arrays of elements and holes to be formed in nanometre range. This can be used to produce 2D PhCs with emitting micro-cavities (missing holes) with lateral size parameters with 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.