A three-dimensional printer and a scanning module thereof is provided. The three-dimensional printer includes a case, a printing platform, a cleaning module, a three-dimensional printing module, a coloring nozzle module and a scanning module. A containing chamber is defined in the case, and a first area and a second area are defined in the containing chamber. The printing platform is arranged in the first area. A portion of the second area is occupied by the cleaning module, and a remaining space is formed by the second area. The three-dimensional printing module and the coloring nozzle module are arranged over the printing platform. The cleaning module is used to clean the coloring nozzle module. The scanning module is arranged in the remaining space. A user obtains a three-dimensional model information of a scanned object via the scanning module, and the three-dimensional printer therefore gains more popularity.

A multi-modal image alignment method includes obtaining first points corresponding to a center vertex of a calibration object and second point groups corresponding to side vertices of the calibration object from two-dimensional images, obtaining third points corresponding to the center vertex from three-dimensional images, performing first optimizing computation using a first coordinate system associated with the two-dimensional images, the first points and the third points to obtain a first transformation matrix, processing on the three-dimensional images using the first transformation matrix to generate firstly-transformed images respectively, performing second optimizing computation using the firstly-transformed images, the first points and the second point groups to obtain a second transformation matrix, and transforming an image to be processed from a second coordinate system associated with the three-dimensional images to the first coordinate system using the first transformation matrix and the second transformation matrix.