The enclosed disclosure relates to a method and apparatus for depositing functionalized nanoparticles within a semiconductor structure in order to create a nano-layer capable of enhancing imaging and contrast, The semiconductor structure can include any type of VNAND structure or 3D structure, The nanoparticles are formed in high-aspect ratio trenches of the structure and form a nano-layer. The functionalized nanoparticles comprise synthesized nanoparticles as well as organic molecules. The organic molecules are chosen to selectively bind to certain nanoparticles and surface materials.