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In this paper, we propose a semi-closed microchip which can realize probe type manipulation in the microchip with the internal environment sealed off from the external environment. The semi-closed microchip has a bath in the middle of microchannel to allow the insertion of micropipettes into the microchip. The bath is sealed off by thin oil film to prevent the evaporation of the solution in the bath. The oil film can seal flexibly even if micropipettes are inserted into the bath and pulled out from the bath by its surface tension. The seal by the oil film was evaluated on the measurement of the weight of the bath after 12/24 hours. Finally, it was demonstrated that the target single cell was harvested by the micropipette in the proposed semi-closed microchip. Long-term experiments can be conducted for in-situ culture and probe type manipulation of cells by the semi-closed microchip. The semi-closed microchip can be used for cell culture, cell analysis and cell harvesting under a microscope as the biological applications for single cell.