This paper introduces a new self-organizing fuzzy logic controller (SOFLC) for precision contour machining in the presence of large disturbances which adjusts both input and output membership functions simultaneously. The parameters of the proposed controller are self-tuned in real-time according to a continuous measurement of the performance of the controller itself and estimated disturbance values. The proposed controller as well as a conventional fuzzy logic controller and a PID controller were simulated and implemented on a 3-axis milling machine in contour milling. Both the simulations and experiments show that the self-organizing fuzzy logic controller has superior performance in terms of contour tracking accuracy compared with the other two controllers.