The vibrational properties of single-wall carbon nanotubes have been probed locally with atomic-scale resolution by inelastic electron tunneling spectroscopy with a low-temperature scanning tunneling microscope. The high spatial resolution has allowed the unraveling of changes in the local phonon spectrum related to topological defects. We demonstrated that the radial breathing mode is suppressed within tube segments of lengths below approximately 3 nm, and that in the cap region phonon modes characteristic of the fullerene hemisphere are emerging. Phonon spectromicroscopy should lead to a better understanding of the mechanisms that limit the transport of heat or electrical charge inside nanostructured carbon materials.