We present the fabrication of large nanodot arrays with very small single dot sizes made of different metals and on different substrates using e-beam lithography and lift-off techniques. Nanodot arrays have a high potential for bioanalytical applications aiming towards single molecule detection. In addition, they can be used as well defined models of heterogeneous catalysts. For this purpose an independent control of the dot size and the distance between the dots is necessary. This is a limitation for many fabrication techniques, which can be overcome by e-beam lithography. However, aiming for the dot size of few tens of nanometers, we observed a strong influence of the beam focusing and astigmatism on the quality of the fabricated nanodot arrays. A significant improvement, i.e. reduction of defect density as well as better control of the dot size, was achieved by modification of the fine focus and stigmation system of the used e-beam writer. Using lift-off technique, we successfully fabricated platinum dot arrays on glassy carbon with target dot diameter ranging from 25 to 35nm. By applying additional annealing step, we could fabricate nanodot arrays made of gold on SiO2 with very small dot sizes down to 6nm and pitch of 100nm. Furthermore, the generation of large area arrays of nanosized pillars was demonstrated using the same exposure strategy in a negative tone HSQ resist.