Hydrocarbon is required to be converted to pure hydrogen without carbon monooxide (CO) for polymer exchange membran fuel cell (PEMFC) applications. In this paper, CO cleaning processes as the downstream of Dimethyl ehter (DME) autothermal reforming process were performed in micro-reactors. Our study suggested two kinds of water gas shift (WGS) reaction process: High Temperature shift (HTS) - Low Temperature shift (LTS), Middle temperature shift (MTS). Firstly, using perovskite catalyst for MTS was decreased effieiciency since methanation. Using HTS-LTS the CO concentration was decreased about 2% ($N_2$ & $H_2O$ free) with the reaction temperature of $420^{circ}C$ and $235^{circ}C$ for HTS and LTS, respectively. As the final stage of CO cleaning process, preferential oxidation (PROX) was applied. The amount of additional oxygen need 2 times of stoichiometric at $65^{circ}C$. The total conversion reforming efficiency of 75% was gained.