We demonstrated a novel technique to fabricate nanosized structures on a Nafion membrane, using thermal nanoimprinting with alinebreak $5 imes 5$,$mu $m$^{mathrm{2}}$ square pattern Si mold without any polymer damage. A 24,MPa thermal imprinting pressure was used for 10,min. We observed high aspect ratio ($sim$1:10) pillars on the surface after imprinting at 200$^{circ}$C. Finally, we used a novel quartz mold with a 200,nm resolution dot pattern.