Towards sapphire and SiC wafer, clear and regular atomic step morphology could be observed all-over the surface via AFM. However, the variations of atomic step widths and step directions are different on the whole of different wafer surfaces: that on sapphire wafer are uniform, while that on SiC wafer are distinct. The effects of atomic step width on removal rate are studied. Removal model of super-hard wafer to realize atomically ultra-smooth surface is proposed. The variations of atomic step morphology toward different defects on sapphire and SiC wafers surface are analyzed, and the formation mechanism is discussed.