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The spatial manipulation of ionic qubits in a fast and precise fashion is one of the foremost issues in scalable quantum information processing with trapped ions.We report our recent efforts toward precise manipulation of trapped ions,including separation,recombination and reordering of the ions,in our home-made microscopic surface-electrode trap.We also demonstrate the micromotion compensation for the trapped ions by rf-photon cross-correlation,which ensures the cooling of the ions down to the temperature 23.3mK.