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Flash memory is widely used because of its shock-resistance and power-efficient features. However, it cannot replace hard disks as secondary storage devices due to their greater cost per unit storage and low capability. In this paper, we propose an energy efficient heterogeneous secondary storage system management scheme for mobile systems. We employ flash memory device as a file cache of hard disk and extend existing data cache management algorithms to distribute files between two devices with consideration of file level cache restrictions. As a result, most file accesses are conducted in flash memory device and disk is spun-down to save energy. We develop a trace-driven simulator to evaluate our scheme in comparison with other alternatives. Results demonstrate that with the help of our scheme, energy consumption of secondary storage system can be saved by up to 90% and I/O access time is improved. Furthermore, the file cache management algorithms can result in high hit ratios.