The synthesis of few-layered graphene is performed by ion implantation of carbon species in thin nickel films, followed by high temperature annealing and quenching. Although ion implantation enables a precise control of the carbon content and of the uniformity of the in-plane carbon concentration in the Ni films before annealing, we observe thickness non-uniformities in the synthesized graphene layers after high temperature annealing. These non-uniformities are probably induced by the heterogeneous distribution/topography of the graphene nucleation sites on the Ni surface. Taken altogether, our results indicate that the number of graphene layers on top of Ni films is controlled by the nucleation process on the Ni surface rather than by the carbon content in the Ni film.