An automated method for aligning 3D (three-dimensional) dental data includes extracting landmark points of a CT (computerized tomography) data, extracting landmark points of scan data of a digital impression model, determining an up vector representing a direction of a patient's eyes and nose and identifying left and right of the landmark points of the scan data, extracting a teeth portion of the scan data, searching a source point of the scan data on a spline curve of the CT data to generate a candidate target point group and determining the candidate target point group having a smallest error with the landmark points of the CT data as a final candidate.