Carbon possesses a number of properties that make it ideal for use in sensor and electrical applications. Using radio frequency plasma with various precursor gases it is possible to prepare carbon surfaces for further molecular attachment or functionalisation. Research in our laboratory has involved studies of plasma fluorination, hydrogenation and methanation of highly ordered pyrolytic graphite (HOPG) (as it serves as a highly ordered, single crystal, model substrate for other more complex forms of carbon), glassy carbon in the form of pyrolysed photoresist films (PPF) and single-walled carbon nanotubes (SWCNTs). Treated surfaces have been characterised using a variety of investigatory surface techniques. In this article we report on results obtained using X-ray Photoelectron Spectroscopy (XPS) for probing the chemical nature of the surface and hence the extent of treatment; Time of Flight Secondary-Ion Mass Spectrometry (ToFSIMS) has been utilised to examine the molecular surface structure and in particular, determine the extent of surface hydrogenation; Scanning Tunnelling Microscopy (STM) measurements provide information on the morphology of treated surfaces, in particular the damage and change in surface structures caused by various plasma treatments. We show in this work that the morphology, mechanisms and extent of modification of the plasma-modified surface obtained is strongly influenced by various experimental conditions. For instance, etching and/or nucleation and growth features are observed, with the type of features and their distribution strongly dependent on the precursor gas that is used to support the plasma. Other important parameters are operating pressure, RF power and exposure time.