The extensive numerical study is conducted to examine interaction of femtosecond pulse laser with thin silicon film structure by using the two-temperature model (2TM) and the three-temperature model (3TM), on the basis of the relaxation time approximation to Boltzmann's transport equation. The present study investigates mainly transient behaviors for carrier number density, electron temperatures, and phonon temperatures, and it compares the results of 3TM with those of 2TM for energy transfer characteristics. In particular, the one-dimensional model is extended to two-dimensional model for the direct estimation of laser-induced crater formation. In addition, the thin film optics and the electromagnetic theory are used to simulate the propagation of laser energy absorption in stratified media with variation of complex refractive index. It is found that quite different tendencies are observed for femtosecond pulse lasers between 2TM and 3TM. For the 3TM, there is clearly nonequilibrium between optical phonons and acoustic phonons when the femtosecond lasers are irradiated, whereas as the laser pulse becomes longer, two different phonons are thermally in equilibrium state. The crater depths and shapes are significantly affected by film thickness, laser fluence, and pulse duration because of the wave interference effect as well as the difference in energy relaxation times. Moreover, the optical properties are found to depend on laser absorption and laser pulses. This tendency which is successfully estimated by the two-dimensional 3TM takes place in thin film structures differently unlike the bulk silicon.