This paper shows the image registering with multi model 3-D medical images by the use of the Matlab inbuilt functions like imregister, imregtform and imwarp to automatically align two volumetric datasets: a CT image and a T1 weighted MR image collected from the same patient at different times. Unlike some other techniques, imregister and imregtform do not find features or use control points. Intensity-based registration is often well-suited for medical and remotely sensed imagery. Also, use imregister to automatically align two magnetic resonance images (MRI) to a common coordinate system using intensity-based image registration. Unlike some other techniques, it does not find features or use control points. Intensity-based registration is often well-suited for medical and remotely sensed imagery.