Cloud cover assessment system and method provides for automatically determining whether a target digital image acquired from remote sensing platforms is substantially cloud-free. The target image is acquired and compared to a corresponding known cloud-free image from a cloud-free database, using an optimized feature matching process. A feature matching statistic is computed between pixels in the target image and pixels in the cloud-free image and each value is converted to a feature matching probability. Features in the target image that match features in the cloud-free image exhibit a high value of feature matching probability, and are considered unlikely to be obscured by clouds, and may be designated for inclusion in the cloud-free database.