In this paper, a fabrication process of a large nanostructure area is introduced and the obtained structures are characterized utilizing SEM stereoscopic technique. The characterization involves 3D reconstruction of nanostructures and surface property calculation. The nanostructures are created by self-assembling a highly ordered monolayer of nanospheres as optical lenses over photoresist to produce deep ordered nano-patterns. Evaluation of these nanostructures is an essential step since the geometry of the primary template affects entire subsequence processes.