Described are computer-based methods and apparatuses, including computer program products, for removing redundant data from a storage system. In one example, a data delineation process delineates data targeted for de-duplication into regions using a plurality of markers. The de-duplication system determines which of these regions should be subject to further de-duplication processing by comparing metadata representing the regions to metadata representing regions of a reference data set. The de-duplication system identifies an area of data that incorporates the regions that should be subject to further de-duplication processing and de-duplicates this area with reference to a corresponding area within the reference data set.