The irradiation of SrTiO3 single crystals with swift heavy ions leads to modifications of the surface. The details of the morphology of these modifications depend strongly on the angle of incidence and can be characterized by atomic force microscopy. At glancing angles, discontinuous chains of nanosized hillocks appear on the surface. From the variation of the length of the chains with the angle of incidence the latent track radius can be determined. This radius is material specific and allows the calculation of the electron– phonon coupling constant for SrTiO3. We show that a theoretical description of the nanodot creation is possible within a two-temperature model if the spatial electron density is taken into account. The appearance of discontinuous features can be explained easily within this model, but it turns out that the electronic excitation dissipates on a femtosecond timescale, too rapidly to feed sufficient energy into the phonon system in order to induce a thermal melting process. We demonstrate that this can be solved if a temperature-dependent diffusion coefficient is introduced into the model.