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Isolation and deposition of specific live cells with the high spatio-temporal resolution from the heterogeneous mixtures are of critical importance to a wide range of biomedical applications. In this paper, we report a robot-assisted cell manipulation tool with optical tweezers based on a uniquely designed microwell array. The whole automatic manipulation includes the target cell recognition, isolation, transportation and deposition. The microwell array is designed based on microfluidics technology, which allows the passive hydrodynamic docking of cells. Image processing technique is used to recognize the target cells based on the cell size or fluorescence label. After recognition, the target cells can be levitated from the microwell, and then assembled by multiple optical traps in parallel. The optically trapped target cells are then transported and deposited to the desired location precisely. Experiments are performed to demonstrate the effectiveness of the proposed cell manipulation approach.