Abstract: A surgical system for operating on a bone of a patient is described. The surgical system includes a reference device including one or more radiopaque markers, a first sensor configured to generate a first signal pertaining to orientation data of the reference device relative to a first coordinate system, a surgical instrument for coupling to an end effector, a second sensor configured to generate a second signal pertaining to orientation data of at least one of the end effector and the surgical instrument relative to a second coordinate system, and a navigation system. The navigation system is configured to determine an orientation of at least one of the end effector and the surgical instrument and superimpose a virtual representation of at least one of the end effector and the surgical instrument over the image based on the determined orientation and user input.