Molecular Dynamics computer simulation is used to demonstrate the behaviour of surfaces upon impact by energetic molecules. At low energies and glancing angles the fullerene molecules can be made to scatter from the surface intact. The coupling of the deposited energy into the surface vibrational modes, particularly for layered materials like HOPG graphite, can lead to what appears to be anomalous behaviour. This is explored and compared with experimental results.Not all fullerene molecules are spherical. The C76fullerene is elliptical in shape. Computer simulations are used to investigate the effects of shape on the scattering of molecules from a graphite surface.Molecular species have been used in ion implantation for doping shallow layers in silicon. There are two contradictory things that can happen when a cluster or molecule is implanted. The molecule will damage the crystal structure with each impact and in so doing could prevent the channelling of the implanted ions, thereby reducing the over‐all range of the implantation. It is also possible that the atoms in the “front” of the cluster/molecule will interact with the surface first, pushing aside the surface atoms so that the atoms of the cluster/molecule following behind might not interact with them so strongly and hence be able to penetrate the solid more deeply. This will result in a deeper implantation range profile. Simulations are compared between single atom and molecular species to investigate which of these mechanisms, if any is operating at low implantation energies.Two clearly observed vibrational modes are excited in a graphite surface by molecular impacts. It is shown that these vibrational modes can assist in the desorption of loosely bound adsorbates from the surface. At higher impact energies it is shown that the surface disruption caused by the impact can both aid and inhibit the desorption process depending upon the position and energy of the initial fullerene impact in relation to the position of the adsorbate. Some simple conclusions about the “desorbing power” of a fullerene impact as a function of energy are drawn. © 2004 American Institute of Physics