Graphite samples exposed to H, D and He plasma at fluencies from 10(16) to 10(18)cm(-2) have been investigated by means of atomic force and Raman microscopies. The ion energy was varied between 40 and 800eV, and the ion incidence was either perpendicular (Highly Oriented Pyrolitic Graphite) or parallel (carbon/carbon composite) to the basal plane. When increasing the impinging ion energy, the growth of nanometric domes at the surface has been observed by atomic force microscopy and the incident kinetic energy has been found as the parameter determining their height. Two different Raman signatures related to (1) a graphitic nano-crystalline component similar to that of a 10(14)cm(-2) bombarded 1-, 2- and 3-layer graphene, and to (2) an amorphous component, have been evidenced. Polarization studies have revealed that these components are related to regions with either in-plane or out-of-plane disorder, coexisting in the material. These Raman studies have also revealed that both the defect-defect distance in the first case and the aromatic domain size in the second case are typically 1nm. When the number of vacancies created in the material increases, the number of in-plane defects decreases to the benefit of the out-of-plane defects. Copyright (c) 2014 John Wiley & Sons, Ltd.