A surgical robotic system is disclosed that provides a combination of a programmed control, such as active control or passive control, when a high degree of accuracy is required and manual control when a high degree of accuracy is not required, such as during the removal of osteophytes, irregular bone growth and/or soft tissue. Manual resection may be completed by switching from the programmed control mode to the manual control mode and allowing the surgeon free control of the cutting tool. The manual resection may be carried out using some navigational features of the robotic system such as allowing the surgeon to visualize the position of the cutting tool thereby allowing accurate resection of osteophytes, irregular bone and tissue while having the unrestricted freedom to move the cutting tool. The programmed control mode may be reserved for procedures that require a high degree of accuracy, for example, the reaming of a bone and placement of an implant onto the bone.