Summary: This paper presents a novel approach for registration of 3D images based on optimal free-form rigid transformation. A proposal consists in semiautomatic image segmentation reconstructing 3D object surfaces in medical images. The proposed extraction technique employs gradients in sequences of 3D medical images to attract a deformable surface model by using imaging planes that correspond to multiple locations of feature points in space, instead of detecting contours on each imaging plane in isolation. Feature points are used as a reference before and after a deformation. An issue concerning this relation is difficult and deserves attention to develop a methodology to find the optimal number of points that gives the best estimates and does not sacrifice computational speed. After generating a representation for each of two 3D objects, we find the best similarity transformation that represents the object deformation between them. The proposed approach has been tested using different imaging modalities by morphing data from Histology sections to match MRI of carotid artery.