A system for controlling the position of an articulated robotic arm includes a robotic catheter procedure system having the articulated robotic arm and a controller coupled to the articulated robotic arm. The system further includes a patient table positioned proximate to and separate from the articulated robotic arm and a tracking system coupled to the controller and configured to measure a change in a position of the patient table. The controller is configured to adjust the position of the articulated robotic arm based on the measured change in position of the patient table.