A scanning electron microscopy system that includes a primary electron beam radiation unit configured to irradiate a first pattern of a substrate having a second pattern formed in a peripheral region of the first pattern, a detection unit configured to detect back scattered electrons emitted from the substrate, an image generation unit configured to generate an electron beam image corresponding to a strength of the back scattered electrons, a designating unit configured to designate a depth measurement region in which the first pattern exists on the electron beam image, and a processing unit configured to obtain an image signal of the depth measurement region and a pattern density in the peripheral region where the second pattern exists, and to estimate a depth of the first pattern based on the obtained image signal of the depth measurement region and the pattern density in the peripheral region.