Self-assembly of colloidal monolayers represents a prominent approach to the fabrication of nanostructures. The modification of the shape of colloidal particles is essential in order to enrich the variety of attainable patterns which would be limited by the typical assembly of spherical particles in a hexagonal arrangement. Polymer particles are particularly promising in this sense. In this article, we investigate the deformation of closely-packed polystyrene particles under MeV oxygen ion irradiation at normal incidence using atomic force microscopy (AFM). By developing a procedure based on the fitting of particle topography with quadrics, we reveal a scenario of deformation more complex than the one observed in previous studies for silica particles, where several phenomena, including ion hammering, sputtering, chemical modifications, can intervene in determining the final shape due to the specific irradiation conditions. In particular, deformation into an ellipsoidal shape is accompanied by shrinkage and polymer redistribution with the presence of necks between particles for increasing ion fluence. In addition to casting light on particle irradiation in a regime not yet explored, we present an effective method for the characterization of the colloidal particle morphology which can be applied to describe and understand particle deformation in other regimes of irradiation or with different techniques.