Understanding and controlling the chemical reactivity of carbon nanotubes (CNTs) is a fundamental requisite to prepare novel nanoscopic structures with practical uses in materials applications. Here, we present a comprehensive microscopic and spectroscopic characterization of carbon nanotubes which have been chemically modified. Specifically, scanning tunneling microscopy (STM) investigations of short-oxidized single-walled carbon nanotubes (SWNTs) functionalized with aliphatic chains via amide reaction reveal the presence of bright lumps both on the sidewalls and at the tips. The functionalization pattern is consistent with the oxidation reaction which mainly occurs at the nanotube tips. Thermogravimetric analysis (TGA), steady-state electronic absorption (UV-vis-NIR), and Raman spectroscopic studies confirm the STM observations.