Dental computed tomography (CT) images and optical surface scan data are widely used in dental computer-aided design systems. Registration is essential if they are used in software systems. Existing automatic registration methods are either time-consuming or rough, and interactive registration methods are experience-dependent and tedious because of a great deal of purely manual interactions. For overcoming these disadvantages, a two-stage registration method is proposed. In the rough registration stage, the rough translation and rotation matrices are obtained by applying unit quaternion based method on the points interactively selected from the two types of data. In the precise registration stage, the stridden sampling is used to reduce computational complexity and the proposed registration algorithm with scale transformation is used for precise registration. The proposed method offers a good trade-off between precision and time cost. The experimental results demonstrate that the proposed method provides faster convergence and smaller registration errors than existing methods.