Currently, semiconductor devices are manufactured in a technology node of several nanometers. Electron microscopy is mainly used in semiconductor inspection in manufacturing stages since accelerated electrons have wavelengths of nanometers or less, and a high spatial resolution can be expected. Among various electron microscopes since the scanning electron microscope (SEM) can observe the sample as it is without processing the sample, the SEM-based inspection instrument is mainly used at each stage of manufacturing the semiconductor device. The paper presents a review of SEM-based electron microscopy in semiconductor inspection. First, an overview of electron microscopy is described to understand the electron-sample interaction, the characteristics of electrons emitted from an irradiated specimen, charging, noise, and so on. Next, application areas such as mask inspection are introduced. Finally, future challenges are discussed.