Based on our earlier works, 10 nm open windows in the SiO2, Si nanowires, and Ge nanowires were fabricated using electron beam induced selective thermal desorption (EB-STD) of SiO2 on Si substrates. In this article, we show that selective etching can be performed with oxygen gas using an SiO2 mask which includes approximately 10-nm-wide open windows formed by STD using focused EB. We also demonstrate the formation of an approximately 10 nm periodic surface structure of Si and SiO2 by STD after irradiation with EB interference fringes. The mechanisms related to these techniques are also discussed. These various methods indicate that EB-STD will be useful for fabricating Si structures of the order of 10 nm.