The JEM-EUSO (Japanese Experiment Module-Extreme Universe Space Observatory) telescope will measure Ultra High Energy Cosmic Ray properties by detecting the UV fluorescent light generated in the interaction between cosmic rays and the atmosphere. Cloud information is crucial for a proper interpretation of these data. The problem of recovering the cloud-top height from satellite images in infrared has struck some attention over the last few decades, as a valuable tool for the atmospheric monitoring. A number of radiative methods do exist, like C02 slicing and Split Window algorithms, using one or more infrared bands. A different way to tackle the problem is, when possible, to exploit the availability of multiple views, and recover the cloud top height through stereo imaging and triangulation. A crucial step in the 3D reconstruction is the process that attempts to match a characteristic point or features selected in one image, with one of those detected in the second image. In this article the performance of a group matching algorithms that include both area-based and global techniques, has been tested. They are applied to stereo pairs of satellite IR images with the final aim of evaluating the cloud top height. Cloudy images from SEVIRI on the geostationary Meteosat Second Generation 9 and 10 (MSG-2, MSG-3) have been selected. After having applied to the cloudy scenes the algorithms for stereo matching, the outcoming maps of disparity are transformed in depth maps according to the geometry of the reference data system. As ground truth we have used the height maps provided by the database of MODIS (Moderate Resolution Imaging Spectroradiometer) on-board Terra/Aqua polar satellites, that contains images quasi-synchronous to the imaging provided by MSG.