We have investigated ultrashort laser micromachining of metals, both from the point of view of the basic physical processes, and the technological implications. The process of hole drilling of Ni with ≈300fs SHG (λ=527nm) Nd-glass and Al samples with 100fs Ti:sapphire (λ=800nm) laser pulses, respectively, has been experimentally addressed by using time-gated optical emission spectroscopy of the ablated material and SEM analysis of the targets. The ablation process has also been analyzed by classical, molecular dynamics (MD) simulations, by using a Morse potential to describe the interaction between the atoms, and taking into account the electron heat diffusion contribution. The dependence of the ablation depth on laser fluence, as measured by SEM analysis, is in good agreement with the numerical simulations and is also well correlated with the optical emission yield of the expanding plume.