The characterization of nanomaterials with complex three-dimensional (3D) geometries is required to further research and enable the continuing development of nanotechnology. In this manuscript, we report a protocol which combines focused ion beam (FIB) milling, thin film deposition and solution chemistry to optimize a rotation holder for 3D structural and chemical analysis of nanoparticles. This protocol is used to customize the geometry, surface and chemistry of a scanning transmission electron microscope (STEM) or transmission electron microscope (TEM) rotation holder for the nanoparticle system of interest. To illustrate this concept, rotation holder stubs were optimized to facilitate the 3D STEM imaging and analysis of core-shell nanoparticles used for DNA detection. Using this approach, it was possible to characterize the morphology, optoelectronic properties and chemical composition of individual core-shell nanoparticles in 3D. STEM images were captured at regular angular intervals over a complete 360 degrees rotation to eliminate missing wedge artifacts. Electron energy-loss spectroscopy (EELS) spectrum images were acquired intermittently for comparative chemical analysis. This approach allows the 3D STEM/TEM analysis to be performed with the nanoparticle of interest cantilevered over vacuum to minimize substrate effects. Standard tomography techniques were used to reconstruct the 3D structure of the individual nanoparticles from the STEM HAADF rotation series. EELS spectrum imaging was used to determine the local material properties such as composition, band-gap and plasmon energy. The nanoparticle analysis protocol reported here can easily be adapted to facilitate 3D TEM/STEM analysis of other nanomaterial systems.