Secondary ion mass spectrometry (SIMS) is a well-known surface analysis technique with numerous applications in materials science. In recent years various types of primary ion beams have emerged to improve SIMS for analysing polymers, organic semiconductors and biological materials. keV cluster ions have given an improvement in producing higher secondary ion yields, reduced topography and reduced interface mixing while MeV SIMS has proven to be better in certain cases especially at desorbing higher mass molecules and has the ability to perform measurements at ambient pressure. This has generally driven the study to understand the interaction between keV cluster ions and MeV ions with insulating materials from both a modelling and an experimental perspective. A simple Monte Carlo model describing the desorption of a molecular solid under keV cluster and MeV ion bombardment is described. The model employs a conical ejection pattern, which has been suggested to be applicable for keV cluster and MeV ions impinging on molecular solids. The conical ejection region is combined with a cylindrical fragmentation region to predict the sputtering behaviour of molecular materials. Molecular dynamics simulations are used to back up this model. The model provides information about surface roughness induced by the process as well as the fragmentation build up during a prolonged sputtering process. This model is expanded to multi-layered systems and has produced some insight on the depth resolution of the analysis. Comparison studies between the model and experiments are also presented with polymer films analysed by a 10keV C60+ time-of-flight (TOF) SIMS. These results are found to compare favourably with each other.