Prostate cancer has been ranked as the second leading cause of cancer death in men. The existence of cancer in prostate is usually examined by a biopsy procedure under the transrectal ultrasound (TRUS) guidance. Development of a prostate biopsy robotics can alleviate urologists' labor and guarantee accuracy. However, it is usually impossible to identify cancer region in the noisy ultrasound images, thus leading to a random biopsy protocol for prostate. It is being recognized that Magnetic Resonance Imaging (MRI) and Magnetic Resonance Spectroscopy Imaging (MRSI) techniques are potential to diagnose cancer distribution in prostate. So navigating the biopsy needle towards those cancer-suspected sites could improve the cancer detection rate and reduce the possibility of false negative diagnosis results. As the prostate usually deforms under the different rectal filling of probes and change of patient postures, a deformable registration scheme is implemented for the integration of the pre-operative MRI/MRSI information with the intra-operative TRUS images. A framework including a global rigid alignment and a sequent non-rigid transformation was described in this paper to match the cross-modal prostate surfaces and thereafter their volumes. For validation, an elastic prostate phantom that simulated the human condition was built up, with fiducial markers implanted inside the phantom prostate as the "ground truth". It shows that our method can achieve at least 30% improvement in accuracy compared with an affine transformation. Preliminary study was also conducted on patient data but with visual assessments presented only due to the current lack of "ground truth".