In recent years, studies on manufacturing systems have proved the importance of cooperation of positioning systems with laser cutting technology. The performance of the manufacturing system can be improved by utilizing both laser and positioning systems together. In this study, modeling and cross coupling controller development of a micromachining system which can perform on non-linear contoured surfaces is presented. Laser micromachining system is designed and assembled including a nanosecond Q-switched pulsed fiber laser, a 6-DOF hexapod manipulator, a granite table in order to absorb vibrations and an external cabin system to isolate the whole system for safety and health issues. The positioning system used here has fast response and precise positioning capabilities with a wide range of workspace. However, its performance of machining non-linear surfaces can be further improved by using a cross coupled control algorithm. On top of the loop based controllers an add-on controller is developed to improve the contouring performance by including the effects of the other feedback loops on the overall controller. Actual laser cutting results also show improvements due to the improvements in the positioning system performance.