The subsonic gas flows through straight rectangular cross-sectional microchannel with patterned microstructures was simulated using the direct simulation Monte Carlo (DSMC) method. An implicit treatment for low-speed inflow and outflow boundaries for the DSMC of the flows in microelectromechanical systems (MEMS) is employed. The 3-D microchannel flows are simulated with the cross-section aspect ratio ranging between 1 and 5. The comparison between 3-D cases and 2-D case shows that when the aspect ratio < 3, the two extra side-walls in the 3-D case have significant effects on the heat transfer and flow properties. When the aspect ratio increases, the flow pattern and heat transfer characteristics tend to approach those of 2-D results. The 2-D simplification is found to be reasonable when the cross-section aspect ratio is larger than 5. The microchannel flows with microstructures are also calculated with three different Knudsen numbers regime cases, and each case is calculated with three different microstructure temperatures, 273K, 323K, and 373K. One Knudsen numbers regime ranges between 0.72 and 1.8, another regime ranges between 0.24 and 0.6 and the other regime ranges between 0.08 and 0.2. The computations show that the cooling and heating effects of the microstructure temperature on flow properties are enhanced with decreasing Knudsen number, and the higher microstructure temperature accelerates the velocity of the flow at the locations above the microstructures.