Multimodal image registration significantly benefits from previous denoising and structure segmentation and vice versa. In particular combined information of different image modalities makes segmentation significantly more robust. Indeed, fundamental tasks in image processing are highly interdependent. A variational approach is presented, which combines the detection of corresponding edges, an edge preserving denoising and the morphological registration via a non-rigid deformation for a pair of images with structural correspondence. The morphology of an image function is split into a singular part consisting of the edge set and a regular part represented by the field of normals on the ensemble of level sets. A Mumford-Shah type free discontinuity problem is applied to treat the singular morphology and the matching of corresponding edges under the deformation. The matching of the regular morphology is quantified by a second contribution which compares deformed normals and normals at deformed positions. Finally, a nonlinear elastic energy controls the deformation itself and ensures smoothness and injectivity. A multi scale approach that is based on a phase field approximation leads to an effective and efficient algorithm. Numerical experiments underline the robustness of the presented approach and show applications on medical images.