In this article a method for reconstructing atmospheric cloud surfaces using a stereo camera system is presented. The proposed camera system utilizes fish-eye lenses in a flexible wide baseline camera setup. The entire workflow from the camera calibration to the creation of the 3D point set is discussed, but the focus is mainly on cloud segmentation and on the image processing steps of stereo reconstruction. Speed requirements, geometric limitations, and possible extensions of the presented method are also covered. After evaluating the proposed method on artificial cloud images, this paper concludes with results and discussion of possible applications for such systems.