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We have developed a simple method to fabricate nanoscale masks by using self-assembly Ni clusters formed through a rapid thermal annealing (RTA) process. The density and dimensions of the Ni nano-masks could be precisely controlled. The nano-masks were successfully applied to GaN-based light-emitting diodes (LEDs) with nano-roughened surface, GaN nanorods, and GaN-based nanorod LEDs to enhance light output power or change structure properties. The GaN-based LED with nano-roughened surface by Ni nano-masks and excimer laser etching has increased 55% light output at 20 mA when compared to that without the nano-roughened process. The GaN nanorods fabricated by the Ni nano-masks and ICP-RIE dry etching showed 3.5 times over the as-grown sample in photoluminescence (PL) intensity. The GaN-based nanorod LEDs assisted by photo-enhanced chemical (PEC) wet oxidation process were also demonstrated. The electroluminescence (EL) intensity of the GaN-based nanorod LED with PEC was about 1.76 times that of the as-grown LED. The fabrication, structure properties, physical features, and the optical and electrical properties of the fabricated devices will be discussed.