Carbon nanofiber (CNF) via interconnect test structures are fabricated with the bottom-up process proposed by Li et al. [Appl. Phys. Lett. 82, 2491 (2003)] for next-generation integrated circuit technology. Critical defects in the interconnect structure are examined using scanning electron microscopy. It is shown that secondary electron signal with optimized incident beam energy is useful for detecting embedded defects, including unexposed CNF plugs and voids in the dielectric layer. The defect imaging mechanisms are elucidated based on beam-induced charging of the specimen surface.