Scanning electron microscopy (SEM) metrology involves significant uncertainty of the linewidth measurement because the SEM image brightness is a complex function of SEM setup, pattern materials, and shape. In this work, the authors used an analytical SEM for critical dimensions metrology applications on a quartz nanoimprint template. The SEM was tuned to find the best condition for consistent operation. Beam characterization was done using BEAMETR beam measurement technique. SEM images of templates were taken at optimum conditions. The measurements were done using two methods: regular imaging processing software based on brightness threshold and using physical model based processing tool myCD. The quartz template was then measured using transmission electron microscopy cross sections at selected sites to reveal profile information as metrology comparison reference. The metrology capability and limitations of analytical SEM with regular image processing were identified. The considerable improvement of accuracy using the physics based image processing was found. (C) 2010 American Vacuum Society. [DOI: 10.1116/1.3504476]