The 3D laser scanning technology was applied to the deformation monitoring of subway tunnel, and for the pre-processing problem of point cloud data, a method of the point clouds filtering with grid handling was studied based on the wavelet analysis. Combining with the scanned point cloud data and its characteristics of Nanjing subway tunnel, this paper analyzed and selected a rational interpolation method to implement the grid processing of the cloud point data. The wavelet transform was used to detect the abnormal values of grid data, and the whole grid data was processed with the threshold de-noising method of wavelet. At last, this study packaged and compared the filtered point cloud data, indicating a very good filtering effect.