The original shaping from shading (SFS) algorithm was adopted to improve the restoring accuracy of the morphology of micro dot. On the basis of the gray image of dot accurately collected by the micro test system, the improved SFS algorithm added with the eight neighboring estimations of the illumination parameters was adopted to construct the 3D resoration of amplitude-modulated dots. Compared to the original algorithm, the improved algorithm accurately and visually constructed the 3D model of the printing dot, which accurately reflected the transferring conditions during the process of printing. The improved algorithm with the estimation of the illumination parameters was an effective tool for 3D restoration of micro dot morphology, which can improve the accuracy of extracting the micro 3D morphology of dots, providing ideas for further control of printing quality.