Several studies have reported on the effectiveness of various disinfection methods for severe acute respiratory syndrome coronavirus 2 and their applicability to the disinfection of N95 respirators and surgical masks. To date, there have been no reports on the decontamination of deep in the intermediate layers of the multilayered structure. In this study, the conditions required for decontamination of such layers were simulated by considering the thickness and shape of N95 respirators or surgical masks (samples). After applying heat (steam, dry heat, or hot water) at 75°C for 60 min or chemical (benzalkonium chloride or laundry detergent) treatment, the collection efficiency of the samples was evaluated. Following the dry heat treatment, the time between the treatment and heat reaching the intermediate layer of the filter fiber was extended by 10 min. A dry heat disinfection method that combines hot water and a closed container was also evaluated, and satisfactory conditions were extended by 60 min. For each heat treatment, there was almost no effect on the collection efficiency, although there were cases where deformation was caused by mechanical stress. In contrast, chemical treatment resulted in a reduction in the collection efficiency of smaller particles.