There is a steadily growing interest in nanostructured coatings, layers and thin films consisting of increasingly complex compounds for their unique structural and functional properties that can be applied to future nuclear technologies. If composition and strain engineering at the nanometer scale should be further adopted in the manufacturing processes of future materials for nuclear applications, there is an obvious need for improvements in the control of these methods and processes and the evolution of these systems under irradiation: the characterization of these effects in thin films of metals, carbides and oxides, possessing various types of nanoscale or mesoscale organization, and in the subsurface characteristics of bulk materials irradiated by ion beams is then a subject needing attention. Glancing incidence diffraction is a sound and non-destructive technique that provides a straightforward way for understanding these systems, as it provides quantitative information about their structures, their microstructures that can be related to the technologically relevant properties. Standards for characterization of these types of materials are not well established yet. In this lecture we discuss the methods and present case studies to illustrate the importance of the specific corrections related to the grazing incidence setup. These corrections are actually implemented in a conventional Rietveld refinement code, XND, freely distributed.