Laser cleaning is a promising surface preparation technique for applications in high value manufacturing industries. However, understanding the effects of laser processing parameters on various types of contaminants and substrates, is vital to achieve the required cleaning efficacy and quality. In this paper, a two-dimensional transient numerical simulation was carried out to study the material ablation characteristics and substrate thermal effects in laser cleaning of aerospace alloys. Element birth and death method was employed to track the contaminant removal on the surface of the material. The result shows that contaminant ablation increases with laser power and number of pulses. The finite element method (FEM) model is capable enough to predict the optimum number of pulses and laser power required to remove various contaminants. Based on the simulation results, the mechanism of the excimer laser cleaning is proposed. Thus, the use of numerical simulation can be faster and cheaper method of establishing the optimum laser cleaning window and reducing the number of experimental tests.