Nowadays, the systems that allow simultaneous employment of both focused electron and ion beams are very important tools in the field of micro- and nanotechnology. In addition to imaging and analysis, they can be used for lithography, which is applied for preparation of structures with required shapes and dimensions at the micrometer and nanometer scale. The first part of the thesis deals with one lithographic method – focused electron or ion beam induced deposition, for which a suitable adjustment of exposition parameters is searched and quality of deposited metal structures in terms of shape and elemental composition studied. Subsequently, attention is paid also to other types of lithographic methods (electron or ion beam lithography), which are applied in preparation of etching masks for the subsequent selective wet etching of silicon single crystals. In addition to optimization of mentioned techniques, the application of etched silicon surfaces for, e.g., selective growth of metal structures has been studied. The last part of the thesis is focused on functional properties of selected 2D or 3D structures.