Silicon nitride (Si3N4) is a very robust material against oxidation and is typically used as an oxidation mask. Here, we report atomic-force microscope (AFM)-based local oxidation Of Si3N4 and its applications in selective-area epitaxial growth using chemical-vapor deposition. High growth selectivity is accomplished in this work by employing a SiO2/Si3N4 bilayer mask structure, which is formed by locally oxidizing the Si3N4 surface (for defining the growth windows), depositing a blanket SiO2 layer, and then selectively removing SiO2 in the growth windows. High-resolution transmission electron microscopy images reveal that the selectively deposited Si structures can be grown with a high degree of crystalline perfection, while excellent size uniformity is confirmed by large-area AFM images.