Atomic force microscopes (AFM) as one of the scanning probe microscopy (spm) modes have become useful tools, not only for observing surface morphology and nanostructure topography but also for fabrication of various nanostructures itself. In this work, silicon oxide (SiOx) patterns were formed on Si(100) surface by means of AFM anodization, where a non-contact mode used to oxidize Si wafer at the nanoscale size. The oxide patterns could serve as masks for the chemical etching of Si surface in alkaline solution in order to create the Si nanodots. A special attention is paid to finding relations between the size of dots and operational parameters as tip bias voltage and tip writing speed Dot arrays with 10 nm high and less than 50 nm in diameter have been successfully fabricated. The ability to control oxidation and scanning speed can be utilized in fabrication of complex nanostructures and make scanning probe lithography (SPL) as a very promising lithographic technique in nanoelectronic devices, nanophotonics and other high-tech areas.