In the present article we report on the selective fabrication of InGaN nanostructures on Si coated GaN/sapphire substrates using the focused ion beam (FIB)/metalorganic chemical vapor deposition (MOCVD) process. InGaN quantum dots and InGaN quantum wires have been fabricated. The process combines window openings in the Si mask layer with localized highly energetic Ga+ FIB irradiation, subsequent photo-assisted wet chemical etching in a solution of KOH:H2O2 (3:1 by mole) and finally the growth of InGaN/GaN nanostructures using MOCVD. This technique proved to be efficient in realizing practically damage-free etching, hence preventing the deterioration of the nanostructure’s crystal quality. The density, size, and positions of the nanostructures could be well designed and controlled using the above process. Structural characterization by transmission electron microscopy, atomic force microscopy observations, and optical investigation by cathodoluminescence were carried out.