In this paper a fabrication process of large area nanostructures is presented. The nanostructure is created by self-assembling a highly ordered monolayer nanospheres as optical lenses over photoresist to produce deep ordered nano patterns. The obtained structure is characterized utilizing SEM stereoscopic technique through 3D-reconstruction of nanostructures. The results show that there are two kinds of deformations. The regular waves of the surface are caused by the embedment of nanospheres to the photoresist. The irregular ups and downs in surface structure could be caused by deposition and UV exposure. The average roughness of the surface is 16.5 nm, indicating that the surface is reasonably smooth. The value of maximum peak to valley distance is 351.8 nm significantly, higher than average surface roughness, which is due to the irregular ups and downs of the surface. Surface properties and geometry of nanostructures are important to their applications, especially when they are used as nano-templates for fabrication of components. Evaluation of these nanostructures is an essential step for intensifying potential nanofabrication problems which improve production quality.