In this paper we demonstrate the possibility of achieving selective epitaxy and epitaxial lateral overgrowth (ELO) using nanometric openings patterned with a focused ion beam (FIB). The test structure we used in this work consists of an AlN buffer layer on 6H–SiC with very high crystal quality close to pseudomorphism. This substrate is first covered with a thin (∼2 nm) silicon nitride mask deposited by CVD. Then a high resolution FIB was used to create regular openings with a range of sizes (lowest 100 nm) and organisation. Finally, GaN was grown on the structure by metal-organic vapour phase epitaxy (MOVPE). The relatively low ion dose (2.7 × 1016 ions/cm2) required to remove the surface layer allows reasonable patterning speeds (0.45 ms/pt) and minimises FIB-induced defect extension in the vicinity of the patterned GaN structures.