This paper presents a versatile system for registering and visualizing computed tomography and magnetic resonance images. The system utilizes a semi-automatic, surface-based registration strategy which has proven useful for registering a number of different anatomical structures. A triangular mesh approximates surfaces in one image set while a set of surface points is used as a surface approximation in the other set. A non-linear optimization procedure determines the transformation that minimizes the total sum-squared perpendicular distance between triangles of the mesh and surface points. This system has been used without modification to successfully register images of the brain, spine and calcaneus.