A system and method for indexing and retrieval of document images in an MMR system having repeated content is described. The system provides one or more hierarchical shared content indices that produce faster and/or more accurate search results. The system is also advantageous because the number and configuration of the hierarchical shared content indices is automated, scalable and efficient for processing documents with partially repeated content. In particular, the MMR matching unit includes a hierarchical shared content index (HSCI) and associated methods of use for processing images where the MMR system includes repeated content. The present invention also includes a number of novel methods including a method for adding an image to a hierarchical shared content index; a method for deleting an image from the hierarchical shared content index, and a method for using the hierarchical shared content index for image recognition, as well as a method for combining multiple MMR indexes into a hierarchical MMR index.