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Existing storage systems using hierarchical directory tree do not meet scalability and functionality requirements for exponentially growing datasets and increasingly complex queries in Exabyte-level systems with billions of files. This paper proposes semantic-aware organization, called SmartStore, which exploits metadata semantics of files to judiciously aggregate correlated files into semantic-aware groups by using information retrieval tools. Decentralized design improves system scalability and reduces query latency for complex queries (range and top-k queries), which is conducive to constructing semantic-aware caching, and conventional filename-based query. SmartStore limits search scope of complex query to a single or a minimal number of semantically related groups and avoids or alleviates brute-force search in entire system. Extensive experiments using real-world traces show that SmartStore improves system scalability and reduces query latency over basic database approaches by one thousand times. To the best of our knowledge, this is the first study implementing complex queries in large-scale file systems.