This paper reports on the effects of growth, transfer and annealing procedures on graphene grown by chemical vapour deposition. A combination of Raman spectroscopy, electrical measurements, atomic force microscopy, and X-ray photoemission spectroscopy allowed for the study of inherent characteristics and electronic structure of graphene films. Contributions from contaminants and surface inhomogeneities such as ripples were also examined. A new cleaning and reconstruction process for graphene, based on plasma treatments and annealing is presented, opening a new pathway for control over the surface chemistry of graphene films. The method has been successfully used on contacted graphene samples, demonstrating its potential for in situ cleaning, passivation and interface engineering of graphene devices. © 2011 Elsevier Ltd. All rights reserved.