The flat plane of small surface roughness below 0.1 μm average roughness was obtained for monocrystalline diamond by nanosecond pulsed laser irradiation of 1060 nm and post-process acid cleaning, at a laser fluence around the material removal threshold value. The glossy and flat plane at the bottom of the micro-groove was parallel to the top surface of the 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 produced a shallower micro-groove with a wider, flatter bottom compared with the round beam in Gaussian mode. The creation method of the 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 did not create a flat plane with constant depth. Therefore, a 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. The newly proposed two-step scanning method was practical and useful to create a widely flat plane with small surface roughness, and the two-step scanning method provided superior control over the micro-groove depth. This proposed method can reduce the surface roughness in addition to the shape creation of monocrystalline diamond, and it can be used as a high-quality micro-shape fabrication method of monocrystalline diamond.