3D scanning is a well-known technology in the cultural heritage field for the study and monitoring of the artworks. For a panel painting, this technology facilitates the acquisition and documentation of its 3D shape at multiple scales, from the micro-geometry of craquelure to the macro-geometry of the support. All these geometric components may change over time due to the deformations induced by the conservation environment parameters. A usual method for estimating the deformation of the panel is the comparison of 3D models acquired at different times. For this purpose, the chapter presents a new approach to automatically estimate the amount of deformation between two 3D models of the same object. The proposed method is based on a nonrigid registration algorithm that deforms a 3D model on the other, enabling to separate the real panel deformation from the structural changes of the artwork. It uses only on the acquired geometric data of independent 3D acquisitions that were uncontrolled and unsupervised over time.