The rear contact solar cell concept has been implemented to increase the solar cell efficiency. Practically, it necessitates rapid fabrication of a large number of via holes to form low-loss current paths. It is not a trivial task to drill a number of microscopic holes through a typical Si wafer of ∼200 µm thickness at reasonable processing throughput and yield. In this research, a femtosecond laser is employed to drill via holes in both crystalline silicon (c-Si) and multicrystalline silicon (mc-Si) thin wafers of ∼170 µm thickness with various laser parameters such as number of laser shots and pulse energy. Since a significantly high pulse energy compared to ablation threshold is mainly applied, aiming to achieve a rapid drilling process, the femtosecond laser beam is subjected to complex non-linear characteristics. Therefore, the relative placement of the sample with respect to the laser focal position is also rigorously examined. While the non-linear effect at high pulse energy regime is complex, it also facilitates the drilling process in terms of achieving high-aspect ratio, for example, by extending the effective depth of focus by non-linear effect. Cross-sectional morphological analysis in conjunction with on-line emission and shadowgraph imaging are carried out in order to elucidate the drilling mechanism.