Micron-sized patterned sapphire substrates (PSS) are used to improve the performance of GaN-based light-emitting diodes (LEDs). However, the growth of GaN is initiated not only from the bottom c-plane but also from the sidewall of the micron-sized patterns. Therefore, the coalescence of these GaN crystals creates irregular voids. In this study, two kinds of nucleation layers (NL)—ex-situ AlN NL and in-situ GaN NL—were used, and the growth of sidewall GaN was successfully suppressed in both systems by modifying the micron-sized PSS surface.