A depth measurement technique for extremely deep holes (such as channel holes in 3D flash memory devices)—by using back-scattered-electron (BSE) images obtained by a high voltage critical dimension scanning electron microscope (CDSEM)— was developed. A high voltage CD-SEM can detect BSEs that penetrate solids surrounding deep holes. These BSE images include rich information concerning the bottom structures of deep holes. As the BSEs lose their energies according to the distance they travel in solids, it is deduced that the BSE image intensity at hole bottoms depends on hole depth. In a feasibility study on depth measurement using an SEM simulator, it was found that the intensity also depends on hole diameter. The relationship between BSE intensity, hole depth, and hole diameter was modeled by simplifying a backscattering model and approximating the target medium by volume density. Based on this model, a depth measurement technique using only a top-view BSE image is proposed. Measurement error of the technique for channel holes of a 3D flash memory device with depths of a few microns was evaluated by using a high voltage CD-SEM. According to the results of the evaluation, error range was 62 nm and measurement repeatability was ± 18 nm. It is concluded that these values are sufficient for detecting depth defects. This technique achieves fast and non-destructive depth measurement of individual extremely deep holes.