In this dissertation, I present the mechanism of graphene hydrogenation via three different electron sources: scanning electron microscopy, e-beam irradiation and H2 and He plasma irradiation. in each case, hydrogenation occurs due to electron impact fragmentation of adsorbed water vapor from the sample preparation process. in the proposed model, secondary and backscattered electrons generated from incident electron interactions with the underlying silicon substrate are responsible for the dissociation of water vapor. Chemisorbed H species from the dissociation are responsible for converting graphene into hydrogenated graphene, graphane. These results may lead to higher quality graphane films having a larger band gap than currently reported. in addition, the dissertation presents a novel and scalable method of controllably removing single atomic planes from multi-layer graphene using electron irradiation from an intense He plasma under a positive sample bias. As the electronic properties or multi-layer graphene are highly dependent on the number of layers, n, reducing n in certain regions has many benefits. for example, a mask in conjunction with this thinning method could be used for device applications.