Molecular dynamics-guided quality improvement in the femtosecond laser percussion drilling of microholes using a two-stage pulse energy process

•Clusters evolution clusters during femtosecond laser drilling is described in detail at the atomic scale.•Based on MD, a two-stage pulse energy (TSPE) percussion drilling process is proposed.•The TSPE femtosecond laser percussion drilling process can effectively reduce the taper of microholes.