A system and method is provided for of characterizing nanostructured surfaces. A nanostructure sample is placed in an SEM chamber and imaged. The system and method locates one of the nanostructures using images from the SEM imaging, excises a top portion of the nanostructure, places said top portion on a substrate such that the nanostructures are perpendicular to the substrate and a base of the top portion contacts the substrate, performs high energy ion beam assisted deposition of metal at the base to attach the top portion to the substrate, SEM imaging the top portions in the SEM chamber, determining coordinates of the top portions relative to the substrate from the SEM imaging of the top portions, placing the substrate in an AFM chamber, and performing AFM imaging of the top portions using the coordinates previously determined.