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Using atomistic modelling, this paper examines the removal behaviours and wear mechanism of GaN at the nanoscale. The diamond tooltip could slide or roll on the crystalline GaN or amorphous/crystalline GaN surfaces at various machining depths. The results indicate that if the machining depth is lower than 4.0 ​Å, the deformation type of the crystalline GaN is elastic. Machining deeper than this depth, the crystalline GaN started to deform plastically. Moreover, increasing the depth results in improving the structure change, stress, and temperature rates. The stress, deformation, and dislocation occur simultaneously. Notably, the wear mechanisms of the crystalline GaN surface strongly depend on the machining depth. The adhering, ploughing, and cutting mechanisms could happen when the tooltip slides over the crystalline GaN surface. In rolling motion, the adhering and ploughing mechanisms could appear during the machining process. Due to the padding function of the amorphous GaN layer, the amorphous GaN layer reduces rates of induced force, stress, structure change, and temperature when compared to the crystalline GaN surface. At the nanoscale, the removal ability of the amorphous GaN layer is higher than the crystalline GaN.