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Applications that query into very large multidimensional datasets are becoming more common. Many self-describing scientific data file formats have also emerged, which have structural metadata to help navigate the multi-dimensional arrays that are stored in the files. The files may also contain application-specific semantic metadata. In this paper, we discuss efficient methods for performing searches for subsets of multi-dimensional data objects, using semantic information to build multidimensional indexes, and group data items into properly sized chunks to maximize disk I/O bandwidth. This work is the first step in the design and implementation of a generic indexing library that will work with various high-dimension scientific data file formats containing semantic information about the stored data. To validate the approach, we have implemented indexing structures for NASA remote sensing data stored in the HDF format with a specific schema (HDF-EOS), and show the performance improvements that are gained from indexing the datasets, compared to using the existing HDF library for accessing the data.