A multi-column scanning electron microscopy (SEM) system is disclosed. The SEM system includes a source assembly. The source assembly includes two or more electron beam sources configured to generate a plurality of electron beams. The source assembly also includes two or more sets of positioners configured to actuate the two or more electron beam sources. The SEM system also includes a column assembly. The column assembly includes a plurality of substrate arrays. The column assembly also includes two or more electron-optical columns formed by a set of column electron-optical elements bonded to the plurality of substrate arrays. The SEM system also includes a stage configured to secure a sample that at least one of emits or scatters electrons in response to the plurality of electron beams directed by the two or more electron-optical columns to the sample.