Zeolites play a crucial part in acid-base heterogeneous catalysis. Fundamental insight into their internal architecture is of great importance for understanding their structure-function relationships. Here, we report on a new approach correlating confocal fluorescence microscopy with focused ion beam-electron backscatter diffraction, transmission electron microscopy lamelling and diffraction, atomic force microscopy and X-ray photoelectron spectroscopy to study a wide range of coffin-shaped MFI-type zeolite crystals differing in their morphology and chemical composition. This powerful combination demonstrates a unified view on the morphology-dependent MFI-type intergrowth structures and provides evidence for the presence and nature of internal and outer-surface barriers for molecular diffusion. It has been found that internal-surface barriers originate not only from a 90 degrees mismatch in structure and pore alignment but also from small angle differences of 0.5 degrees-2 degrees for particular crystal morphologies. Furthermore, outer-surface barriers seem to be composed of a silicalite outer crust with a thickness varying from 10 to 200 nm.