We have quantitatively investigated a periodic nanostructure exposure process by electron beam lithography (EBL). The targeted applications are nano- to micro-electromechanical systems (NEMS/MEMS), nanophotonics, surface plasmonic structures, and metamaterials. It is confirmed that the character projection (CP) method can obtain both high throughput and high resolution simultaneously as compared with the variable-shaped beam (VSB) method. We used square, triangular, and octagonal CP stencil masks to realize a nanohole array (NHA) of 10.4 mm2 area. The holes were placed in both square and hexagonal grid configurations. We measured the hole patterns by scanning electron microscopy (SEM) and scanning probe microscopy (SPM). Also, the effect of NHA size variation was measured on the basis of optical absorption spectra obtained using a system consisting of an optical microscope and a spectrum analyzer. The spectrum variation was confirmed to be in good agreement with the local size variation; identically fabricated NHAs showed identical spectra. It is therefore possible to control the nanometric critical dimensions by using NHAs as process indicators.