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In this paper, an automatic system for single cell analysis inside an environmental scanning electron microscopy (ESEM) was proposed. Single yeast cell was put on an tungsten probe substrate inside ESEM. The endeffector for single cell analysis was fixed to an nanorobotic manipulator, which has three degrees of freedom, i.e. X, Y and Z translation. The real time images during the experiment can be observed by ESEM system in realtime. Therefore, the position of the endeffector and the single cell can be recognized by imaging processing. These position information were used as the feedback signal to control the movement of the nanorobotic manipulator. Finally, a single cell cutting experiment was performed to demonstrate the working mechanism of this system. Two types of cell pattern substrates were also designed and fabricated as the cell analysis chips for the automation single cell analysis in the future.