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.