We study the instability of nanometric Cu thin films on SiO2 substrates. The metal is melted by means of laser pulses for some tens of nanoseconds, and during the liquid lifetime, the free surface destabilizes, leading to the formation of holes at first and then in later stages of the instability to metal drops on the substrate. By analyzing the Fourier transforms of the SEM (scanning electron microscope) images obtained at different stages of the metal film evolution, we determine the emerging length scales at relevant stages of the instability development. The results are then discussed within the framework of a long-wave model. We find that the results may differ whether early or final stages of the instability are considered. On the basis of the interpretation of the experimental results, we discuss the influence of the parameters describing the interaction of the liquid metal with the solid substrate. By considering both the dependence of dominant length scales on the film thickness and the measured contact angle, we isolate a model which predicts well the trends found in the experimental data.