Direct methanol fuel cell (DMFC) is considered as a candidate for portable power sources, that could overcome the disadvantages of lithium battery. But in order to attain commercial viability the long term stability of the DMFC should be achieved. Understanding the long-term behavior of membrane-electrode assembly (MEA) is a prerequisite to this purpose and the optimization of the MEA is also needed. In this study we have investigated the changes in performance and electrochemical properties of the MEA during extended operation and the effects of heat treatment of MEA on the long-term performance. The MEAs have been treated in an autoclave with saturated water vapor at 120$^{circ}C$, vacuum oven at 140$^{circ}C$ and boiling in organic solvents. The autoclaved MEA was found to be have the best long term performance. The on-off operation mode also increased the performance probably due to effective removal of products from the electrodes. Physical and electrochemical analyses using a scanning electron microscope, impedance analyser and half-cell technique have been done to characterize the MEAs.