In film processes, many actuators and scanning sensors are utilized to control film properties. Multi-loop controllers are applied to the pairs of actuators and scanned data because they can be tuned without the precise process models. The selection of the measurement location corresponding to an actuator is not easy because the film is stretched and its edges are cut off. It is illustrated that inadequate pairing causes deterioration of the multi-loop controller performance. A method based on wavelet analysis is proposed to detect inadequate pairing and to prevent the deterioration of the controller performance.