Interaction of hydrogen atoms with highly oriented pyrolytic graphite (0001) surface at near room temperature was studied by means of thermal programmed desorption (TPD), atomic force (AFM) and scanning tunneling (STM) microscope. Bubbled surfaces were observed after irradiation of graphite with atomic hydrogen. The average height of bubbles was about 3-5 nm and the lateral size up to 100 nm. AFM and STM tips are not only used for surface imaging but also for destruction of bubbles. The possibility of bubble destruction with STM and AFM tips without noticeable traces of remaining substance of the bubbles on the surface, and a flat bottom of the produced craters may be regarded as a further support in favor of our previous hypothesis of hydrogen intercalation between upper graphite layers.