We report on high-resolution transmission electron microscope structural studies of InAs colloidal semiconductor nanocrystal quantum dots (NCQDs) on ultrathin GaAs (001) semiconductor single-crystal substrates. We employ a benign method for preparing electron transparent specimens that is suitable for the study of such fragile samples. The image contrast comprises contributions from electron scattering from both the NCs and the GaAs substrate. Long-term electron exposure studies reveal different damage mechanisms operative in the nanocrystals and the substrate.