Due to the SARS-CoV-2 pandemic, it is crucial to study the efficiency of face masks in retaining viruses for the upcoming years. The first objective of this study was to validate a method to elute viruses from polyester and cotton face masks. We observed that deionized water followed by 3% beef glycine (pH 9.5 or pH 7.2) was significantly more efficient (p < 0.05) in eluting the bacteriophage phiX174 virus from polyester (4.73% ± 0.25% to 28.67% ± 1.89%), polyester/cotton (3% ± 0.33%), and cotton (1.7% ± 0.21%) face masks than 3% beef glycine only (pH 9.5 or pH 7.2) as a single eluent (3.4% ± 0.16% to 21.33% ± 0.94% for polyester, 1.91% ± 0.08% for polyester/cotton, and 1.47% ± 0.12% for cotton face masks). Also, deionized water was significantly less efficient as a single eluent for eluting bacteriophage phiX174 from all the studied face mask types. The polyethylene glycol (PEG) precipitation method was substantially more efficient (p < 0.05) as a second step concentration method for the viruses in the eluates than the organic flocculation (OF) method. Higher viral loads were eluted from polyester face masks than cotton ones. We also found varying viral loads in the eluate solutions from different commercial polyester face masks, with the highest percentage seen for the N95 face mask. The second objective was to apply the validated method to study the effect of autoclaving on the different face mask materials. Results of the study did not show any significant differences in the viral loads eluted from the studied face masks before and after one and five autoclaving cycles. Moreover, a scanning electron microscope (SEM) analysis revealed no changes in the yarns, elongation, tensile strength, and contact angle measurements of the polyester or cotton materials after one or five autoclaving cycles.