There is a great deal of interest in the functionalization, in particular fluorination, of single-wall carbon nanotubes (SWNTs) for the purposes of solvation and subsequent chemical reaction. Towards this end, this thesis reports the investigation of fluorinated SWNTs (fluorotubes) performed by scanning tunneling microscopy (STM). This research was performed for various compositions of fluorinated nanotubes. In addition, the atomic-scale fluorine coverage on the fluorotubes with composition was observed as a function of annealing temperature. Upon heating of the fluorotubes, we observe the subsequent desorption of the fluorine initiated around 240°C. At higher temperatures all the fluorine desorbs from the tubes revealing a few "defects" still remaining. Further heating leads to cutting of the fluorotubes which we believe is initiated at these defect locations. Through these studies we gain important information on the local chemistry as well as the electronic structure of the functionalized carbon nanotubes.