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In tunnel inspections, it is important to check for the progression of cracks and other deformations. The point clouds of tunnels are not reproducible due to accumulated errors in mobile mapping systems using GNSS/IMU navigation. Therefore, it has been impossible to confirm the progression of deformations with the original point cloud because the shapes of the acquired point clouds do not match. Therefore, the position of the point cloud has been corrected by surveying or by manual alignment of the point cloud. This was time-consuming and costly. In this paper, we propose a new positioning method for two-time difference comparisons based on a scan-matching technique that matches tunnel features and describe the evaluation results. The results of evaluation experiments show that the average error before alignment was 0.831 m. The proposed method achieves alignment with an average error of less than 0.040 m, which is unprecedentedly accurate.