A computer-assisted surgery system allows a user to control movements of a surgical tool by providing, to a control unit, inputs in the form of measured displacements via a movable part of a handle while treating a region of interest with the tool. The control unit is configured to enable motion of the tool with respect to an anatomical structure only if a user moves the movable part, receive the measured displacement of the movable part, receive from a localization unit the relative position and orientation of the tool relative to the anatomical structure, based on the measured displacement, on the surgical plan and on the relative position and orientation of the tool relative to the anatomical structure, compute an instruction to send to a motorized joint to move a robotic arm to operate the tool according to an optimal trajectory, and send the computed instruction to the motorized joint.