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Background: There is a need for sensor-guided robotic devices that discriminate working conditions and media, and control interaction of tool-points with respect to tissues. At the micro-surgical scale the need is to control exact penetration through flexible tissues and to control relative motion with respect to moving or deforming tissue targets and interfaces., Methods: This paper describes a smart surgical drill that is able to control interaction with respect to the flexing tissue to avoid penetration or to control the extent of protrusion with respect to the position of the flexible tissue interface under drilling. The sensing scheme used is able to discriminate between the variations in types of conditions posed in the drilling environment., Results: The fully autonomous system is able to respond to tissue type, behaviour and deflection in real time. The system is robust in terms of different drilling angle, thickness, stiffness, and disturbances encountered. Also it is intuitive to use, efficient to set up and uses standard drill bits., Conclusions: The smart drill has been used to prepare cochleostomies in theatre and was used to remove bone tissue leaving the endosteal membrane intact. This has enabled preservation of sterility and the drilling debris to be removed prior to insertion of the electrode. Results presented in this paper suggest that the robotic smart drill is tolerant and robust on various angled drilling trajectories with respect to tissues, tissue thickness, environmental disturbances, and has been used within the operating theatre., (Copyright © 2012 John Wiley & Sons, Ltd.)