CT colonography (CTC) is a minimally invasive screening technique for colorectal polyps and colon cancer. Through the addition of prone scanning with the original supine scanning, the possibility of detecting the polyps is increased. Thus, the comparison between the prone and supine colons is required for diagnostic purposes. A piece-wise centerline matching algorithm and, the interpolation and extrapolation methods of deformation field are presented in this paper for highly accurate deformable registration. By incorporating these two methods into a modified demons algorithm, registration accuracy is enhanced even though there are severe deformations between prone and supine colons