Scanning tunneling microscopy (STM) is an ideal tool for probing the chemistry and physics of these types of nanostructures. Building upon on our previous carbon nanotube research, we have investigated thiol and thiophene sidewall functionalized single-walled carbon nanotubes (SWNTs). The motivation is to use these functional groups as a means to self-assemble tubes on surfaces by exploiting the well-established Au-S chemistry. Thiol and thiophene substituted nanotubes were self-assembled on bare gold surfaces as well as inserted into hexanethiol self-assembled monolayers and imaged by STM. The thiol and thiophene functional groups work as anchors, strongly binding the SWNTs to the gold. Additionally, we have measured the size and spatial distribution of the functional groups along the nanotube sidewalls. Furthermore, we have extended this self-assembly technique to biological applications where individual fullerene-terminated peptide molecules have been successfully imaged by STM with the help of insertion into close-packed alkanethiol monolayers.