There is considerable interest in mitigating secondary electron emission (SEE) from surfaces and electrodes produced by incident electrons, due to the deleterious effects of SEE in vacuum electron devices, accelerators, and other technologies. Since surface conditions are known to affect SEE, here the role played by crystal orientation and a vacancy (which is a simple example of a surface defect) is probed through Monte Carlo simulations. The effect of the lattice imperfection on the frequency-dependent permittivity, which then influences inelastic energy losses, mean free paths, and secondary generation profiles, is obtained on the basis of density-functional theory. The Monte Carlo simulations are in good agreement with previous experimental reports. The results indicate that the secondary electron yield for pure copper is the highest for the 110 orientation and the lowest for the 111 case, with a relatively higher differential predicted between a single vacancy and ideal copper for the 111 orientation. The results underscore the benefit of annealing or reducing inhomogeneities through laser or charged particle beam surface treatments.