Dendrimers have shown great potential in drug delivery because of their enhancement of drug solubility in aqueous media, leading to an increase in in vivo circulation and efficacy to targets. The structure of drug-dendrimer complexes however, is not well-known owing to the difficulties associated with visualizing individual drug molecules attached to dendrimers. Scanning tunneling microscopy (STM) enables visualization of dendrimer intramolecular structures using our approach of metal ion tagging. This work extends the approach to reveal the hierarchical structure of indomethacin-loaded poly(amidoamine) hydroxyl-terminated dendrimers. STM imaging provides structural information such as their height, lateral dimensions, and volume. High-resolution STM images enable the identification and count of individual indomethacin molecules bound to the anterior of dendrimers. Removal of drug molecules by the STM tip allows the calculation of individual drug-dendrimer binding energy, which is consistent with 1-3 hydrogen bonds. These investigations provide new insight into the hierarchical structure and nature of indomethacin-dendrimer interactions and deepen our understanding of the stability and pharmacokinetic behavior of dendrimer-based drug delivery vehicles.