Patterning of metal oxide nanostructures with different shapes and well-defined size may play an important role in the improvement of MEMS systems, sensors and optical devices. We investigated the effects of HSQ e-beam resist processing on the fabrication of sputtered TiO2 nanostructures. They were patterned using direct write e-beam lithography combined with ICP-RIE etching in CF4/Ar plasma. Experimental results confirmed that the HSQ resist with a thickness of about 600 nm is suitable as a masking material for optimal etching process and allows patterning of the dots array in TiO2 sputtered films with a thickness up 150 nm. TiO2 arrays with a minimal dots diameter of 180 nm and spacing of 1000 nm were successfully developed.