This paper gives a brief review of our recent work on a new method of nanoscale pattern formation of thin oxide film on Si substrate by using a scanning tunnelling microscope (STM): A field-emitted electron beam (e-beam) extracted from the STM tip is used for selective removal of the oxide film by e-beam-induced reduction and thermal annealing at moderately high temperatures (300-700 °C). The process is dependent on electron dose and the patterning is controllable by adjusting the emission current and exposure time. One can draw nanoscale open-window patterns directly on oxide-covered Si substrates, e.g. lines and concentric circles of a few tens of nanometres in line width and spacing. Such patterning on the Si oxide layer shows good reproducibility and flexibility of the nanofabrication method, which suggests a further development and application of this method in nanotechnology. The beam profile of the extracted e-beam is measured and the beam-energy dependence of the quantum yield of the process is derived. Based on the excitation function, we consider that the decomposition is activated by core-level excitations as is the Knotek-Feibelman mechanism. One can also make use of this technique to diagnose the Si/SiO2 interface topography on a sub-nanometre scale.