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Dispersion of metal nanoparticles on flat surfaces has attracted considerable interest in many technological applications. Numerous advantages of functionalized patterned nanostructures especially in medical physics, chemistry, biology, and semiconductor quantum dot applications have rapidly driven the growth of this field in the last two decades. In particular, for applications involving biomedical imaging, the nanoparticles have attracted perhaps the greatest attention as these materials provide a direct interface at the subcellular length scale. Reliable characterization methods are thus often needed to infer their detailed structural properties such as average particle size, particle shape, internal structure, surface morphology, distribution of particles, and their chemical composition. As a nondestructive probe, X-ray fluorescence measurements at grazing incidence provide sensitive information about the physical and chemical nature of the nanoparticles over the large surface area of a substrate. Herein, we demonstrate the potential capabilities of the X-ray fluorescence technique for reliable and precise determination of surface morphology of metal nanoparticles, dispersed on a flat surface. Our results show that X-ray standing wave assisted fluorescence measurements are markedly sensitive to the nature of dispersion of nanoparticles on a substrate surface. We have analyzed different types of nanostructured materials; e.g. a W thin film structure and Au nanoparticles deposited on a Si surface. The average size of the Au nanoparticles estimated, using X-ray standing wave fluorescence analysis, was found to closely agree with the atomic force microscopy measurements. The inherent features of the X-ray fluorescence technique permit us to analyze distribution of all kinds of metal and metalloid nanoparticles on a flat surface. Copyright © 2017 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]