Block copolymers auto-organize on dense area of 5-50 nanometers nano-objects. By adjusting parameters like molecular weight, it is possible to auto-organize spheres, cylinders, or lamellars in organic matrix. The self-assembly of block copolymers have been studied to realize silicon nanowires for nanoelectronic applications. Cylinders pattern of PS-block-PMMA system is transferred by using plasma etching. Because the pattern height is around 10 nm, different strategies are proposed depending on the depth to transfer into silicon. One strategy describes diblock copolymers / gold interaction and shows that the morphology of gold nanostructures can be controlled by using different plasma treatments. Otherwise, for nanowires transistor fabrication, it is necessary to align the direction of PMMA cylinders which follow random directions. The graphoepitaxy method is investigated to align cylinders and use diblock copolymer pattern as etching mask.