The pulse train effects on femtosecond laser material processing are investigated from the viewpoint of electron dynamics on dielectrics with fused silica as a case study and metals with Al as a case study in air and water. During femtosecond laser (800 nm, 35 fs) pulse train (double pulses per train) processing of fused silica, a non-monotonic relationship between ablation size and pulse separation is observed with an abrupt rise in the range of 150–275 fs. It is assumed that this is due to the enhancement of photon–electron coupling efficiency and transition of the phase-change mechanism by adjusting the free electron density during pulse train ablation. Surface quality in Al is improved with less recast by designing the pulse energy distribution to adjust the electron/lattice temperature distribution. Furthermore, the positive effects on ablation quality by femtosecond pulse train technology are more significant in water than those in air.