A metrology system includes front and back vision components portions. The front vision components portion includes a light source, camera, variable focal length (VFL) lens, and objective lens defining an optical axis. The back vision components portion may include a reflective surface and a polarization altering component. A workpiece with apertures is located between the front and back vision components portions. For each aperture of the workpiece, the system adjusts a relative position between the front vision components portion and the workpiece to align its optical axis with each aperture such that light from the light source passes through the aperture and is reflected by the reflective surface of the back vision components portion. The system uses the VFL lens and camera to acquire an image stack including images of the aperture, and analyzes the image stack to determine a measurement related to a workpiece feature of the aperture.