We investigated a gradient of nanometer-sized, self-assembled gold clusters on top of a thin polymer film. Using an advanced characterization method for gradient surfaces and thin films, the characteristic change in cluster height is detected. Our unprecedented approach combining a powerful thin-film characterization method with a micrometer-sized x-ray beam enhances the spatial resolution used thus far by two orders of magnitude. We show that this advanced concept allows for a nondestructive and contact-free reconstruction of the three-dimensional structure and morphology of the nanocluster gradient layer. Despite its change in thickness, the individual clusters’ in-plane shape and distance remains constant.

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