In this work, we report the direct methanol fuel cell (DMFC) performance of micro-patterned (μp) Nafion® 117 (N117) membranes prepared by hot embossing and compare them with that of normal N117 and heat and pressure treated (hp) N117 non-patterned (smooth) membranes. Our results suggest that the heat and pressure treatment during hot embossing probably makes the membrane structure more compact and decreases the membrane swelling due to decrease of amount of freezable water in the membrane. This leads to lower methanol flux for both hp N117 and μp N117 membranes in comparison to the non-patterned N117. Nonetheless, all three membranes have similar electrical resistance because they probably have the same amount of non-freezable water. Non-freezable water is the one which is strongly bound to the ionic groups and facilitates the proton transport and it is not influenced by the heat treatment. In the DMFC, the hp N117 has rather similar performance with normal N117 membrane despite its lower methanol crossover. The μp N117, however, has better performance than normal N117 probably due to better catalyst utilization by the micro-pattern. In DMFC stacks, which contain multiple MEAs, this can lead to a higher power output gain and/or lower system volume.