Molecular dynamics simulation examines how the polishing tool's rotating velocity and axes affect surface nanotribological properties and material removal mechanism of patterned gallium nitride (GaN) substrates. Frictional coefficient and average contact area affect material removal rate (MRR) variance. Rotating speed increases the frictional coefficient and contact area, elevating MRR. Anticlockwise abrasives have substantially higher root-mean-square roughness (RMS) than clockwise ones. After polishing, increasing the rotating angle increases the frictional coefficient, average contact area, MRR, and RMS. MRR enhancement is maximum at −15 rad/ns, the only spinning velocity that improves MRR. RMS improvement ratio is highest when the polishing tool spins clockwise or the rotational axis orientation is lowered. Particularly, the MRR and RMS improvements after the polishing process can reach 103.8 % and 223.5 %, respectively. These findings help explain atomic-scale GaN-based material removal and deformation with frictional resistance and erosion by polishing.