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The effect of microwave hydrogenated (MW-H) plasma exposure on the morphology of mechanically polished natural single crystal (100) oriented diamond type 2a surfaces is reported. It is shown that the surface morphology is very sensitive to plasma power and exposure time. Under appropriate plasma exposure conditions the diamond surfaces smooth out as reflected in the decrease in the number and depth of the polishing lines. A systematic study of the influence of hydrogen MW plasma power and exposure time on the diamond surface morphology is presented. The morphology of the diamond surfaces at the different stages was monitored with sub-nanometric resolution by atomic force microscopy and scanning electron spectroscopy.