Gases in microfluidic structures or devices are often in a non-equilibrium state. The conventional thermodynamic models for fluids and heat transfer break down and the Navier-Stokes-Fourier equations are no longer accurate or valid. In this paper, the extended thermodynamic approach is employed to study the rarefied gas flow in microstructures, including the heat transfer between a parallel channel and pressure-driven Poiseuille flows through a parallel microchannel and circular microtube. The gas flow characteristics are studied and it is shown that the heat transfer in the non-equilibrium state no longer obeys the Fourier gradient transport law. In addition, the bimodal distribution of streamwise and spanwise velocity and temperature through a long circular microtube is captured for the first time.