In this paper, a new system for navigated control in functional endoscopic sinus surgery (FESS) is presented. The system allows the safe and convenient use of a shaver that can be enabled by the surgeon only within a specified working space. Preoperatively, the surgeon defines this working space in the axial slices of the CT scan. During the surgery, the positions of the shaver and patient are tracked by an optical navigation system, which calculates whether the shaver is within the working space. The navigated control electronics receives a signal from the navigation system and disables the shaver if it is outside the working space. If the shaver is inside the working space, the surgeon can set its speed freely with a foot pedal. Experimental evaluation shows that the system allows convenient and intuitive safe removal of inflamed tissue while protecting sensitive structures. The clinical applicability was proven in a clinical trial with 10 patients.