Recent advances in the compound beam positioning technology that incorporates acousto-optic deflectors (AODs) have demonstrated a superior capability in improving the process throughput and quality in industrial laser-based via drilling. For instance, an innovative intra-pulse steering approach for CO2 laser-based via drilling has been developed to drill blind-via-holes to form multi-layer interconnects in High-Density-Interconnect (HDI) substrates. However, the complex nature of process dynamics in laser-based via drilling makes it challenging for rapid process development. Aiming to help to minimize the time and cost for process development, we utilize 3D multiphase simulations to provide physical insights into various laser micromachining applications. In particular, we explore the underlying physical mechanisms during CO2 laser via drilling in both traditional laser punch process and intra-pulse steering process enabled by AODs. The simulation results highlight the influence of the hydrodynamic motion of copper melt during the laser via drilling process and provide useful physical insights for further improvement of process quality.