Abstract The ultra-thin 2 in. diameter silicon (1 1 1)-H(1 × 1) wafer appeared to be a promising material for a mirror focusing He-atom beam in a scanning atom microscope. To increase achievable at present resolution from 1.5 μm to a sub-micron range the 50 μm thick (1 1 1) silicon wafer with thickness distribution better than ±1 μm and 0.05° precision of miscut value is necessary. The purpose of this paper was to adapt X-ray measurements to control the miscut value with high precision for the 50 μm thick silicon wafers as well as to control the deviation of the wafer surface from ideal flat plane by measurements of low-angle reflection using X-ray high resolution diffractometer (HRXRD). The crucial point was the construction of a stress-free ultra-thin wafer holder. The precision of 0.01° miscut value was obtained. The deviation of the surface from the ideal flat surface obtained by X-ray measurements were compared with the one estimated from optical (confocal) method. A satisfactory good conformity between both methods has been observed.