Nowadays, more and more scientists are working on paintings’ restoration and deformations’ detection. There are plenty of non-destructive testing methods to analyze a painting and many algorithms that calculate differences between two models of different periods of time (epochs). In this manuscript, after measuring paintings in different epochs, using a coordinate measuring arm or a laser tracker, specific steps are followed to calculate the deformations with an accuracy of ± 0.10 mm. The Cloud-to-Cloud Distance (C2C) or the Multiscale Model to Model Cloud Comparison (M3C2) algorithm can calculate two or three-dimensional deformations which are useful for restorers. So, in this research, after using these algorithms, a three-dimensional deformation model is created to help restorers, before, during or after restoration process. This methodology is tested in two different paintings and important results concerning the deformation models are obtained.