The subject disclosure is directed towards data deduplication (optimization) performed by phases/modules of a modular data deduplication pipeline. At each phase, the pipeline allows modules to be replaced, selected or extended, e.g., different algorithms can be used for chunking or compression based upon the type of data being processed. The pipeline facilitates secure data processing, batch processing, and parallel processing. The pipeline is tunable based upon feedback, e.g., by selecting modules to increase deduplication quality, performance and/or throughput. Also described is selecting, filtering, ranking, sorting and/or grouping the files to deduplicate, e.g., based upon properties and/or statistical properties of the files and/or a file dataset and/or internal or external feedback.