Uncertainty in gauge block measurement depends on three major areas, thermal effects, dimension metrology system that includes measurement strategy, and end standard surface perfection grades. In this paper, we focus precisely on estimating the uncertainty due to the geometrical imperfection of measuring surfaces and wringing gab in calibration of end standards grade 0. Optomechanical system equipped with Zygo measurement interferometer (ZMI-1000A) and AFM technique have been employed. A novel protocol of measurement covering the geometric form of end standard surfaces and wrung base platen was experimentally applied. Surface imperfection characteristics of commonly used 6.5 mm GB have been achieved by AFM in 2D and 3D to be applied in three sets of experiments. The results show that there are obvious mapping relations between the geometrical imperfection and wringing thickness of the end standards calibration. Moreover, the predicted uncertainties are clearly estimated within an acceptable range from 0.132 µm, 0.164 µm and 0.202 µm, respectively. Experimental and analytical results are also presented.