We have proposed an alignment system for low-energy electron-beam lithography. The proposed alignment system is based on the following unique concepts: (1) an alignment mark is detected using voltage contrast images caused by charging, and (2) to improve the alignment accuracy of global alignment, the alignment accuracy can be inspected before the pattern exposure without any loss of time. In order to verify these concepts, we performed a series of experiments. Using an electron beam of a few keV, we detected a mark buried by thick insulator films; even if direct access to the marks by the primary beam is prevented, the mark detection is possible. Also, we confirmed that the simultaneous observation of exposure patterns and alignment mark is possible using the voltage contrast images caused by charging: the inspection is possible for the exposure status without resist development.