In this study, we used femtosecond laser-assisted etching (FLAE) to drill through glass vias (TGVs) in 0.3 mm thick non-alkali glass substrates. In FLAE, the focus of the femtosecond laser pulses is scanned to modify the material along a preprogrammed pattern, and the modified region is preferentially removed by chemical etching. We found that the scanning strategy affected the etching rate along the laser-modified lines. Among four types of scanning strategies tested, the strategy 〈du〉—that is, scanning in a downward direction followed by an upward direction—obtained the highest etching rate. In this case, the etching rate along the laser-modified line was approximately 10 times larger than that of the unmodified region.