A wireless handheld user input device may be moved within six degrees of freedom in order to generate position data that describes the position and angular orientation of the user input device within three-dimensional space. Position data is received by a position management device and is interpreted to reduce the input data from six degrees of freedom down to a number of degrees of freedom that is supported by a surgical instrument adapted to be manipulated by a robotic surgical system. Position data is interpreted by taking raw overlap data showing the change from a baseline position to a current position and correcting it to zero out inputs for unsupported degrees of freedom that do not exceed a device or device portion specific threshold. The converted overlap data may then be used to generate new joint target positions, which may be communicated to the robotic surgical system.
