A technique for efficiently scanning various datasets in a storage system to generate metadata for shared data blocks is provided. In one embodiment, data containers in an active file system of a storage object are first scanned. Remaining images (e.g., snapshots of the file system) are arranged in a chronological order based on the age of such images in the storage object. In some instances, to perform a metadata scan of a given image, the storage server compares each data container in the given image to a corresponding data container in a prior image (from the chronological order) to identify any non-identical data blocks (i.e., blocks that are not common between the data containers of the two images) in each data container. The metadata scanner then generates metadata only for the non-identical data blocks in each data container and skips metadata generation for any remaining data blocks.