Present research paper represents that the intra organelle nano poration of multi layer osteoblast cell placed in a 3D non uniform micro fluidic chip composed of bi metallic heterogeneous micro electrode under the influences of smart control FPGA based pico pulse generator and images of intra organelle nanoporation are recognized experimentally. It is observed that When the micro pulse is applied the cell starts to response but it is unable to penetrate the intra cellular nucleus- membrane where as the expected results will come when the Pico pulse is applied on the cell, a number of nano pores are generated on the intra organelle and chemicals are entered into the cell. It is also exposed that the key parameter of nanoporation such as intra pore density and ion uptake are externally controlled by user defined hybrid 3D micro chip and FPGA based pico pulse generator