We studied by means of an atomistic model based on molecular dynamics the thermal evolution of surface atoms in amorphous silica under high electronic excitation produced by irradiation with swift heavy ions. The model was validated with the total and differential yields measured in sputtering experiments with different ions and ion energies showing a very good quantitative prediction capability. Three mechanisms are behind the evolution of the surface region: (1) an ejection mechanism of atoms and clusters with kinetic energy exceeding their binding energy to the sample surface, which explains the experimentally observed angular distributions of emitted atoms, and the correlation of the total sputtering yield with the electronic stopping power and the incidence angle. (2) A collective mechanism of the atoms in the ion track originated by the initial atom motion outwards the track region subsequently followed by the return to the resulting low-density region in the track center. The collective mechanism describes the energy dissipation of bulk atoms and the changes in density, residual stress, defect formation and optical properties. (3) A flow mechanism resulting from the accumulation and subsequent evolution of surface atoms unable to escape. This mechanism is responsible for the crater rim formation.