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MEMS-based storage is anticipated to be used as the secondary storage of mobile consumer devices due to its attractive features such as small size, low-power consumption, and low cost. However, physical structures of MEMS-based storage are vastly different from traditional hard disks especially in the way of data placement and seeking. Hence, it is important to revise the software management techniques appropriate for MEMS-based storage. In this paper, we present a new I/O scheduling algorithm for MEMS based storage called G-MST that exploits the two-dimensional graph algorithm and group-based SCAN. The proposed algorithm aims at reducing the total seek distance in the two dimensional MEMS structure and providing fast and uniform response time simultaneously. Simulations with synthetic and real world I/O traces are performed to assess the effectiveness of G-MST.