The present disclosure provides a system and method for controlling an articulating member including a tool. The system may include a dual camera system that captures near-infrared (NIR) images and point cloud images of a tissue or other substance that includes NIR markers. The system may generate a three-dimensional (3D) path based on identified positions of the NIR markers, may filter the generated path, and may generate a 3D trajectory for controlling the articulated arm of a robot having a tool to create an incision along the filtered path. In a shared control mode, an operator may generate manually control commands for the robot to guide the tool along such a path, while automated control commands are generated in parallel. One or more allocation functions may be calculated based on calculated manual and automated error models, and shared control signals may be generated based on the allocation functions.