3D dynamic contrast enhanced magnetic resonance (MR) images may help to reduce the high re-excision rate associated with breast conserving surgery. However these images are acquired prone, whilst surgery is performed supine which results in a large deformation that limits their usefulness. We describe here a registration technique based on a biomechanical model to account for soft tissue deformation between prone MR imaging and surgery. The accuracies of the individual registration steps are assessed off-line. We then report our first clinical experience with an image-guided surgery system which incorporates these algorithms. The system's accuracy is assessed against tracked ultrasound images, and is determined to be around 5mm for this case.