This paper describes a robust three-dimensional (3D) surface reconstruction method that can automatically eliminate shadowing errors. For modeling shadowing effect, a new shadowing compensation model based on the angle distribution of backscattered electrons is introduced. Further, it is modified with respect to some practical factors. Moreover, the proposed iterative shadowing compensation method, which performs commutatively between the compensation of image intensities and the modification of the corresponding 3D surface, can effectively provide both an accurate 3D surface and compensated shadowless images after convergence.