This paper investigated the effects of femtosecond laser beam polarization on ablation efficiency and microstructure symmetricity for 64FeNi alloy (Invar) sheet processing to fabricate fine metal masks. It was found that the ablation efficiency for linear polarization was approximately 15% higher than that for circular polarization due to electric field enhancement induced by low-spatial-frequency laser-induced periodic surface structures (LIPSS). The hole size and sidewall taper angles for the microstructures generated by linear polarization were asymmetric, whereas those generated by circular polarization were symmetric due to non-oriented LIPSS. The asymmetric and symmetric three-dimensional microstructure profiles, measured by using a confocal laser scanning microscope, were verified by employing an analytical model that was derived using the total input fluence and the ablation rates for linear and circular polarizations, respectively.