In this paper we present an analysis of medical images based on robot kinematics. One of the most important problems in robot-assisted surgeries is associated with the medical image registration of surgical tools and anatomical targets. The fundamental problems of contemporary frame-based image registration are that the registration fails in case of incomplete data in the image and the registration algorithm depends on the shape, assembly, and number of fiducials. To solve the registration problem in the situation where a cylindrical end-effector of surgical robots operates inside the patient’s body, we developed a numerical method by applying robot kinematics knowledge to cross-sectional medical images. Our method includes a 6-D registration algorithm and a cylindrical frame with four helix and one straight line fiducials. The numerical algorithm requires only a single cross-sectional image and are robust to noise and missing data, and are algorithmically invariant to the actual shape, number, and assembly of fiducials. The algorithm and frame are introduced in this paper, and simulation results are described to show the adequate accuracy and resistance to noise.