The multiscale noise in the 3D point cloud data of rock surfaces which collected by 3D scanners has a significant influence on the exploration of rock surface morphology. To this end, this paper proposes a multiscale noise removal overall filtering algorithm. The specific processing procedure of the algorithm is as follows. First, a weighted principal component analysis is performed on point cloud data, i.e., the neighboring point distance is used as a weight in the principal component analysis, the covariance feature matrix of the weighted point is estimated, and the eigenvector corresponding to the lowest eigenvalue is used as the normal vector of the point cloud data. Second, in the weighted principal component analysis, estimating three eigenvalues corresponding to the Eigen matrix of the point cloud data, the ratio of the eigenvalue corresponding to the normal vector to the sum of three eigenvalues is used as the surface change factor. For the sample point, if the surface change factor of one sample point is less than the average value of the surface change factor of all sample points in the neighborhood, the sample point belongs to a flat area; otherwise, it belongs to a mutation area. Finally, in order to achieve multiscale noise removal, statistical filtering algorithm is used to remove large scale noise in flat area, additionally bilateral filtering algorithm is adopted to remove small scale noise in mutation area. In the experiments, the improved principal component analysis is combined with the overall filtering algorithm to accurately estimate the eigenvalues of the point cloud data points. After that, the eigenvalues of the sample points are used to distinguish between flat area and mutation area, so as to consider large scale noise and small scale noise. From the experimental results, it can be seen that overall filtering algorithm can consider both large scale and small scale noise and can remove noise from the point cloud data of rock samples. Visual judgment, normal distribution and fractal distribution tests are employed on filtered rock sample point cloud data to verify the reliability of the filtering results.INDEX TERMS 3D scanner, point cloud data, multiscale noise, statistical filtering, bilateral filtering.