It's not easy, especially if it's a 3D image. There are lots of complicated papers on the process. For starters, why don't you start with cpselect(), a simple, manual 2D registration using user-selected landmarks. In the help, navigate to this discussion: Image Processing Toolbox -> User's Guide -> Image Registration -> Registering an Image.
Another option is Brett Shoelson's http://www.mathworks.com/matlabcentral/fileexchange/34510-image-registration-gui
Thanks Image Analyst.. I tried the code with cpselect. After running the program, how to find whether the image has been registered.
If you are using R2012a, you might also check out the new function imregister. This function can be used to perform automated image registration: