Several factors affect the safe operation of a bio-mechatronic system such as design limitations of the robots to do complex surgical manoeuvres, malfunction of the system’s components, unpredictability of the working envelope to name a few. One measure that can be taken in order to improve the safe performance is to implement a reliable control system. In our research, an optimal control hierarchy and strategy is considered for implementation for non-invasive surgical applications. A control strategy is proposed for supervisory hybrid control using PID and model-based robust control as the parameterized controllers and its implementation for FUSBOTBS (a custom designed robotic system using Focused Ultrasound Surgery for Breast Surgery) is demonstrated. Mechanical feasibility tests and in-vitro experimental trials supported the results with a positioning accuracy within 0.5mm.