We have applied digital holography (DH) as interferometric tool for measuring the out of plane deformation of Micro-Electro-Mechanical structures. DH has been adopted as method for determining with high accuracy deformations due to the residual stress introduced by fabrication process evaluating MEMS behavior subjected to thermal load. A thermal characterization of these structures requires to cope two fundamental problems. The first one regards the loss of the focus due to thermal expansion of the MEMS sample support. With an out-of-focus image, a correct reconstruction of the sample image can not be obtained. To overcome the problem an auto-tracking procedure has been adopted. The other problem regards the direct comparison of images reconstructed at two different distances. In fact, in DH the numerical reconstruction image is enlarged or contracted according to the reconstruction distance. To avoid this problem, we have adopted a novel but very simple method for keeping constant the image size by imposing the reconstruction pixel constant through the fictitious enlargement of the number of the pixel of the recorded digital holograms. These procedures have been employed in order to characterize MEMS with different shapes and dimensions. The measured profiles obtained by DH can be employed to evaluate both the residual stress induced during the fabrication processes and its dependence on the temperature.