A three-dimensional molecular dynamics model is presented for the simulation of the creation of a micro-hole on a thin film metal substrate via laser ablation. For the presented analysis, molybdenum and aluminium specimens are selected and short pulses are assumed. The laser fluence takes several values between 0.5 and 20 J/cm². The proposed models include significant laser ablation phenomena such as plasma shielding. However, they are not computationally intense. In this study, the Morse potential is used for the interactions of the atoms of the specimens. The analysis is carried out in order to investigate the ablation rate, the ablation depth and the mean temperature of molybdenum and aluminium targets under their heating by the laser beam, for several different values of fluence. Results for molybdenum indicate that as fluence increases, it takes less time for the atoms to be ablated. For low-fluence pulses, more than one pulse may be required for the ablation of all atoms. For high-fluence pulses, the ablation is not uniform across the entire duration of the pulse and the specimen is overheated. A fluence value around 2–3 J/cm² is suggested for uniform ablation. From the analysis, it is evident that the evolution of ablation and system temperature is different for molybdenum and aluminium, for the same laser fluence. This is attributed to different crystalline structures and absorptivity of each material. It may be said that molecular dynamics prove to be a powerful tool for the simulation of nanomanufacturing processes and useful conclusions are drawn from the analysis.