With the advantages on non-equilibrium heating and desorption induced by electronic transition, the femtosecond pulse laser introduces a new way for solving the problem of impurity pollution adsorbed on a solid thin film in micro-electro-mechanical systems (MEMS). A model based on stochastic processes was established for stimulated desorption induced by the femtosecond pulse laser to interpret the interaction of the optically excited hot electrons with the adsorbed molecules in a metal substrate. Numerical simulation results reveal a time-dependent desorption probability of adsorbed molecules and indicate that how key parameters of femtosecond pulse laser, such as incident laser energy flux, pulse duration, and wavelength of pulse, have a great effect on the desorption probability.