We present a novel method to register three-dimensional echocardiography (echo) images with magnetic resonance images (MRI) based on anatomical features, which could be used in the registration pipeline for overlaying MRI-derived roadmaps onto two-dimensional live X-ray images in electrophysiology (EP) procedures. The features used in image registration are the surface of the left ventricle and a manually defined centerline of the descending aorta. The MR-derived surface is generated using a fully automated algorithm, and the echo-derived surface is produced using a semi-automatic process. We test our method on six volunteers and three patients. We validated registration accuracy using two methods. The first calculated a root mean square distance error using anatomical landmarks. The second method used catheters as landmarks in one clinical EP procedure. Results show a mean error of 4.24 mm, which is acceptable for our clinical application, and no failed registrations were observed. In addition, our algorithm works on clinical data, is fast and only requires a small amount of manual input, and so it is applicable to use during EP procedures.