The use of Finite Element meshes in Digital Image Correlation (FE-DIC) is now widespread in experimental mechanics. Up to now FE have been much less used in Stereo-DIC. The first goal of this paper is to explain in details how to use FE in Stereo-DIC using a formulation in the physical coordinate system. More precisely, it is shown how to perform the calibration of possibly nonlinear models, shape and displacement measurement based on a FE mesh. In addition it is shown that with such a framework it is possible to regularise the measurement with a FE model based on the same mesh. For instance, using this technique, it is shown that it is possible to measure the rotation field of a bending plate in addition to its displacement.