Nanostructured materials are increasingly subject to nearly every type of chemical and physical analysis possible. Due to their small sizes, there is a significant focus on tools with high spatial resolution. It is also natural to characterize nanomaterials using tools designed to analyze surfaces, because of their high surface area. Regardless of the approach, nanostructured materials present a variety of obstacles to adequate, useful, and needed analysis. Case studies of measurements on ceria and iron metal-core/oxide-shell nanoparticles are used to introduce some of the issues that frequently need to be addressed during analysis of nanostructured materials. We use a combination of tools for routine analysis including X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), and x-ray diffraction (XRD) and apply several other methods as needed to obtain essential information. The examples provide an introduction to other issues and complications associated with the analysis of nanostructured materials including particle stability, probe effects, environmental effects, specimen handling, surface coating, contamination, and time.