The flat plane of small surface roughness below 0.1 µm average roughness could be obtained for monocrystalline diamond by nanosecond pulsed laser irradiation of 1060 nm and post-process of acid cleaning, at the laser fluence around the threshold value of material removal. The glossy and flat plane at the bottom of micro-groove was parallel to the top surface of specimen, although the round beam of Gaussian-mode was irradiated in the direction perpendicular to the top surface of specimen. The square beam of top-hat mode could obtain shallower micro-groove with wide flat bottom in comparison with the round beam of Gaussian mode, and then the creation method of flat plane with small surface roughness was discussed in the arrangement strategy of linear micro-grooving by the square beam of top-hat mode. Normal side-by-side repetition of linear micro-grooving could not create the flat plane of a constant depth. Therefore, two-step scanning method was proposed in order to overcome the problem in the normal side-by-side repetition of liner micro-grooving. Non-removal areas were partly retained between the processing lines in the first step, and the laser scanning was conducted on the retained area in the second step. Newly proposed two-step scanning method was practical and useful to create a wide flat plane with small surface roughness, and the controllability of micro-groove depth could be improved by the two-step scanning method. This proposed method can reduce the surface roughness in addition to the shape creation of monocrystalline diamond, and it can be used as the high-quality micro-shape fabrication method of monocrystalline diamond.