Recently a growing interest has been seen in minimally invasive treatments with open configuration magnetic resonance (Open-MR) scanners. In this paper, we proposed a semi-automatic non-rigid 3D MR-CT image registration technique for MR-Guided Liver Cancer Surgery in which cancer tissues are coagulated by microwave ablation. Because of the lower magnetic field (0.5T) and various different surgical conditions, sometimes tumors can not be visualized clearly on Open-MR volumes. Combining of CT volumes acquired before surgery, it is possible to identify the tumor's location by application of registration techniques. Since such a registration problem belongs to a non-rigid one considering the easy deformation of livers, free-form deformation (FFD) based registration method is applied. Similarity measurement in registration is normalized mutual information (NMI). Both phantom and clinical experiments show that the registration is