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Three-dimensional fuzzy logic controller (3-D FLC) is a novel FLC developed for spatially distributed parameter systems. In this study, we are concerned with data-based 3-D FLC design. A nearest neighborhood clustering algorithm is employed to extract fuzzy rules from input-output data pairs, and then an optimization algorithm based on geometric similarity measure is used to reduce the obtained rule base. The consequent parameters are estimated using linear support vector regression. Finally, a catalytic packed-bed reactor is taken as an application to demonstrate the effectiveness of the 3-D FLC.