Nanomanipulation with Atomic Force Microscopy (AFM) is one of the fundamental tools for nanomanufacturing. The motion control of the nanomanipulation system requires accurate feedback from the piezoelectric actuator and a highfrequency response from the control system. Since a normal AFM control system for scanning motion is not suitable for control of arbitrary motion, we therefore modified the hardware configuration to meet the demand of nanomanipulation control. By identifying the necessary parameters using system identification methods, we built up a new dynamic model for the modified configuration. Based on the new model and configuration, we designed and implemented a control scheme as motion controller for AFM nanomanipulation operation. The aims are to analyze various factors in the control of the AFM-based nanomanipulation system. By integrating the original AFM controller with the external Linux real-time controller, we achieved a stable system with high-frequency response. Several problems have been addressed based on the new control scheme, such as high frequency response, robust feedback control and non-linearity, etc. Finally this Multiple-Input Single-Output (MISO) system is validated by a real-time nanomanipulation task. It is proved to be an effective and efficient tool for the controlling of the nanobiomanipulation operation by cutting the intercellular junction of human keratinocytes.