We report on cross-sectional transmission electron microscope (TEM) observations using a novel TEM specimen preparation. The processes of the method are presented in detail. In this approach, carbon nanotubes (CNTs) can be conserved in the state in which they were correlated with the substrate during the growth. The results directly confirm that the CNTs grow in a base-growth mode. Chemical analyses on the cross-section of the structures were also carried out. A new type of bulk defect or void was observed for the first time.