Abstract We present a ‘top-down’ patterning technique based on ion milling performed at low-temperature, for the realization of oxide two-dimensional electron system devices with dimensions down to 160 nm. Using electrical transport and scanning Superconducting QUantum Interference Device measurements we demonstrate that the low-temperature ion milling process does not damage the 2DES properties nor creates oxygen vacancies-related conducting paths in the STO substrate. As opposed to other procedures used to realize oxide 2DES devices, the one we propose gives lateral access to the 2DES along the in-plane directions, finally opening the way to coupling with other materials, including superconductors.