In recent years, the importance of intracellular material introduction technology is increasing. Our large scale cell membrane perforation method is a new cell modification technique. The feature of this perforation method is efficient in order to make the perforation to the group of cells, with high cell survival ratio. The problem on the current technique is, only limited part of the sequential process is automated. The target of this research is to automate sequences of operations associated with the cell modification. As the result, we could successfully construct the system for the automation and shorten the whole process time from 3-4 hours to 45min.