A system for treating tissue during a medical procedure with an instrument, the system being for use with a navigation system adapted to determine a position and orientation of said instrument relative to a virtual boundary associated with the tissue being treated and comprising: the instrument (200, 1200), with the instrument being adapted to be manually supported and moved by a user, and said instrument (200, 1200) including a hand-held portion (500; 1204) adapted to be held and supported in the hand of a user, a working portion (202, 204) movably coupled to said hand-held portion (500; 1204), a plurality of actuators (220, 222, 224; 1240, 1302, 1304) operatively coupled to said working portion (202, 204) for moving said working portion (202, 204) in a plurality of degrees of freedom relative to said hand-held portion (500; 1204), and a plurality of sensors for sensing positions of said working portion (202, 204) relative to the hand-held portion; and a control system in communication with said actuators (220, 222, 224; 1240, 1302, 1304) to control said actuators (220, 222, 224; 1240, 1302, 1304) to move said working portion (202, 204) relative to said hand-held portion (500; 1204) to maintain a desired relationship to the virtual boundary associated with the tissue being treated, said control system being configured to establish a home position of said working portion (202, 204) relative to said hand-held portion (500; 1204) and track deviation of said working portion (202, 204) from the home position as said working portion (202, 204) moves in one or more of the plurality of degrees of freedom relative to the hand-held portion (500; 1204) in order to maintain a desired relationship to the virtual boundary, wherein the control system is configured to control a cutting speed of the working portion (202, 204) based on the deviation. the instrument (200, 1200), with the instrument being adapted to be manually supported and moved by a user, and said instrument (200, 1200) including a hand-held portion (500; 1204) adapted to be held and supported in the hand of a user, a working portion (202, 204) movably coupled to said hand-held portion (500; 1204), a plurality of actuators (220, 222, 224; 1240, 1302, 1304) operatively coupled to said working portion (202, 204) for moving said working portion (202, 204) in a plurality of degrees of freedom relative to said hand-held portion (500; 1204), and a plurality of sensors for sensing positions of said working portion (202, 204) relative to the hand-held portion; and a control system in communication with said actuators (220, 222, 224; 1240, 1302, 1304) to control said actuators (220, 222, 224; 1240, 1302, 1304) to move said working portion (202, 204) relative to said hand-held portion (500; 1204) to maintain a desired relationship to the virtual boundary associated with the tissue being treated, said control system being configured to establish a home position of said working portion (202, 204) relative to said hand-held portion (500; 1204) and track deviation of said working portion (202, 204) from the home position as said working portion (202, 204) moves in one or more of the plurality of degrees of freedom relative to the hand-held portion (500; 1204) in order to maintain a desired relationship to the virtual boundary, wherein the control system is configured to control a cutting speed of the working portion (202, 204) based on the deviation.