Low-cost, high-throughput and nondestructive metrology of truly three-dimensional (3D) targets for process control/monitoring is a critically needed enabling technology for high-volume manufacturing (HVM) of nano/micro technologies in multi-disciplinary areas. In particular, a survey of the typically used metrology tools indicates the lack of a tool that truly satisfies the HVM metrology needs of 3D targets, such as high-aspect-ratio (HAR) targets. Using HAR targets here we demonstrate that through-focus scanning optical microscopy (TSOM) is a strong contender to fill the gap for 3D shape metrology. Differential TSOM (D-TSOM) images are extremely sensitive to small and/or dissimilar types of 3D shape variations. Based on this, we here propose a TSOM method that involves creating a database of cross-sectional profiles of the HAR targets along with their respective D-TSOM signals. Using the database, we present a simple-to-use, low-cost, high-throughput and nondestructive process-monitoring method suitable for HVM of truly 3D targets, which also does not require optical simulations, making its use straightforward and automatable. Even though HAR targets are used for this demonstration, the similar process can be applied to any truly 3D targets with dimensions ranging from micro-scale to nano-scale. The TSOM method couples the advantage of analyzing truly isolated targets with the ability to simultaneously analyze many targets present in the large field-of-view of a conventional optical microscope.