In this paper, a novel control methodology for a micro injection mechanism with a permanent magnet synchronous motor (PMSM) is presented. The shaft of the motor is formed by micro pipette holder which houses the injection pipettes for piercing. The aim of the control system is to generate smooth oscillation at the tip of micro glass pipette with adjustable frequency and amplitude. These rotational oscillations facilitate the pipette to pierce the membrane of the cell with minimal biological damage and material consumption. Simulations are conducted to verify the performance of the proposed control methodology. Experiments demonstrate that with designed mechanical structure and control system tracking of rotational motion is achieved in accordance with total micro-drilling task.