To reduce skin irritation and allergic symptoms caused by long-term mask use, we produced a mask with a filter effect by laminating nanofibers on habutae silk fabric, a specialty of Japan’s Fukui Prefecture, using the electrospinning method. We investigated the filter characteristics of silk fabrics with different weave structures (habutae, flat crepe, and twill). We found that woven fabrics alone could not sufficiently block particles finer than 1 μm, even when the fabric layers were overlapped. Therefore, we had a nanofiber filter layer fabricated on the surface of habutae fabric by the electrospinning method at a weight of 1 g/m2. The nanofibers removed more than 94% of 0.3 μm-particles, which are similar to the size of virus particles. However, the nanofiber layer was so dense that it caused an increase in pressure drop, so we made the nanofiber layer thinner and fabricated the filter on the surface of the habutae fabric at 0.5 g/m2. A three-dimensional mask consisting of two woven fabrics, one with a nanofiber layer on the inside and the other with a normal woven fabric without a nanofiber layer on the outside, was fabricated and tested on 95 subjects. The subjects reported that the nanofiber habutae masks were more comfortable than nonwoven masks. Moreover, the silk woven masks did not cause allergic symptoms such as skin irritation.