A few questions: For the 6 dof robotic arm, do you mean the subsystem in this example?: https://www.mathworks.com/help/control/examples/multi-loop-pid-control-of-a-robot-arm.html Or is there another block you are referring to?
If you are talking about the above, then presumably you could just use some coordinate transformations inside the subsystems "6Dof Robot Arm". If you wanted to input world frame coordinates as the control input, then you'd do these coordinate transformations in your controller before the signal reaches your actuators.
