The paper presents aspects connected with development of a computer system for registration and fusion of multimodal images for orthodontic purposes. The idea of the system, of the multimodal image registration, lies in 3D surfaces registering, reconstructed from the sets of MRI or CT planar slices. The system enables the user to perform registration using different approaches based on localised landmarks, based on selected regions of 3D surfaces or based on automatic matching of the whole surfaces. The rigid-body transformation found during the registration is then used to transform the set of slices to generate images that can be fused. The usage of the system was illustrated and the accuracy of the registration was assessed.