Abstract: A medical system includes a robotic arm, a surgical cart, a setup arm, and an alignment unit. The setup arm is mounted to the surgical cart and is configured to operatively couple to the robotic arm. The alignment unit is operatively coupled to the setup arm and configured to determine the orientation of the robotic arm relative to a representative coordinate system. A method of aligning a robotic arm with a representative coordinate system includes projecting an alignment pattern from an alignment unit onto a horizontal surface such as the floor, patient, or representative coordinate system, wherein the alignment unit is operatively coupled to a setup arm mounted to a surgical cart. A user is then prompted to manipulate the alignment pattern by adjusting the alignment unit. An input indicating that adjustments to the alignment unit are complete is then received.