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Large crystals of zeolite ferrierite (FER) are important model systems for spatially resolved catalysis and diffusion studies, though there is considerable variation in crystal habit depending on the chemical composition and employed synthesis conditions. A synergistic combination of techniques has been applied, including single crystal X-ray diffraction, high-temperature in situ confocal fluorescence microscopy, fluorescent probe molecules, wide-field microscopy and atomic force microscopy to unravel the internal architecture of three distinct FER zeolites. Pyrolyzed template species can be used as markers for the 8-membered ring direction as they are trapped in the terraced roof of the FER crystals. This happens as the materials grow in a layer-by-layer, defect-free manner normal to the large crystal surface, and leads to a facile method to diagnose the pore system orientation, which avoids tedious single crystal X-ray diffraction experiments., (© 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)