We report an investigation into the magnetic and electronic properties of partially hydrogenated vertically aligned few layers graphene (FLG) synthesized by microwave plasma enhanced chemical vapor deposition. The FLG samples are hydrogenated at different substrate temperatures to alter the degree of hydrogenation and their depth profile. The unique morphology of the structure gives rise to a unique geometry in which graphane/graphone is supported by graphene layers in the bulk, which is very different from other widely studied structures such as one-dimensional nanoribbons. Synchrotron based x-ray absorption fine structure spectroscopy measurements have been used to investigate the electronic structure and the underlying hydrogenation mechanism responsible for the magnetic properties. While ferromagnetic interactions seem to be predominant, the presence of antiferromagnetic interaction was also observed. Free spins available via the conversion of sp2 to sp3 hybridized structures, and the possibility of unpaired electrons from defects induced upon hydrogenation are thought to be likely mechanisms for the observed ferromagnetic orders.