The design of coordinate measuring machines (CMM) has undergone a radical change in recent years with the aim of improving its speed and measurement accuracy. The enhanced performance is achieved by substituting the analogue component with high speed digital processors and the mechanical components by high power electronic devices. The control system is, however, hardly changed from the conventional PID controllers and heuristic tuning practices. The controller design to fully utilise the power of these new machines is a major challenge since the two conflicting performance requirements of speed and accuracy should be simultaneously satisfied. To ensure the total control of the system, four interacting feedback loops, (the current, the velocity, the position and the vibration loops) for each arm, and one feedforward loop, (profile loop) need to be designed, implemented and tuned. This gives a total of 15 control loops for the three arms. Unlike the conventional control system where the controlled variable is available for feedback, the probe position is difficult and expensive to measure. The objective of this paper is to develop an optimal CMM controller such that the speed and the measurement accuracy of this machine may be maximised while the tuning and commissioning time may be minimised. The proposed control design scheme uses a hierarchical approach to decompose the system into smaller subsystems. The current and velocity loops are firstly optimised. It is then shown through extensive modelling and simulation that the MIMO control problem can be decoupled into three SIMO control problems. A two DOF optimal controller is then developed to control the probe position and the arm vibration. The feedforward controller is automatically generated by introducing the model of the profile in the control design scheme. Simulation and experimental results show that the optimal controller can significantly reduce the probe position deviation and also minimise the positioning time using only a high speed servo actuator for each arm.