Low-pressure microplasma treatment was performed to clean a substrate surface prior to the selective growth of GaN by chemical beam epitaxy. To investigate the cleaning mechanism, the process pressure and process time were systematically varied. The plasma distribution was also studied using a special sheet, whose color changes following the irradiation of plasma species. Consequently, it was found that the range of microplasma irradiation increased with decreasing process pressure, and simultaneously, the morphology of selective growth was improved. Secondary ion mass spectrometry measurements show that the oxygen concentration at the growth interface was reduced from 9.7 × 1014 to 2.6 × 1013 atoms/cm2 by the microplasma treatment. Otherwise, the surface oxides resulted in the growth of a rough surface with the suppression of the layer-by-layer growth.