1. A method for moving a substrate to a predetermined location with a specified orientation with a robotic manipulator, the robotic manipulator having a plurality of joint actuators and an end-effector for holding the substrate, wherein the end-effector is independently rotatable with respect to the remaining robotic manipulator, the method comprising the steps of: selecting a reference point on the end-effector for determining a position of the end-effector, wherein the reference point is offset from a wrist of the robotic manipulator; determining a motion path for movement of the reference point on the end-effector of the robotic arm toward a predetermined location with a specified orientation; generating motion profiles for translation of the reference point on the end-effector along the motion path and rotation of the end-effector with respect to the reference point; and converting the motion profiles into joint motion profiles for each of the joint actuators of the robotic manipulator for implementing the movement of the end-effector to the predetermined location with the specified orientation.