The results of graphene layers formation on Ni surface due to methane pyrolysis are presented in this work. The investigation was carried out using technique that allows controlling morphology of the sample surface with high spatial resolution. This technique includes the use of scanning tunnel microscope (STM) introduced inside the reaction chamber which allows to get rid of atmosphere gases impact. Bubble structure of obtained few-layer graphene film with typical diameter about 100 nm was observed. It was found that local morphology of these bubbles can be easily changed by increasing tunnel voltage applied to the STM tip.