In the simulation of secondary electron yields (SEY) and secondary electron microscopy (SEM) images, there is always the question: "are we using the correct scattering cross-sections?". The three scattering processes of interest are quasi-elastic phonon scattering, elastic Mott scattering and inelastic scattering using the dielectric function model. We have artificially scaled the scattering cross-sections, such that the probability for events associated with a particular model is either increased or decreased. The influence of this adjustment on the calculated SEYs and simulated SEM images is then evaluated. At first we have investigated the influence on the calculated SEY of pure and infinitely thick silicon. We have observed that the influence of the (quasi-elastic) acoustic phonon scattering cross-sections is seen all the way up to the incident primary electron energy of 10 keV. We have extended the analysis to the simulation of SEM images of three dimensional rough lines of PMMA located on a silicon substrate. We conclude that the scaling of the scattering cross-sections affects the contrast of the SEM images, but not the roughness characterization of the lines, i.e. the 3σ of the LER, correlation length and roughness exponent.