The development and applications of a two-dimensional DSMC (Direct Simulation Monte Carlo) program for pressure boundaries using unstructured cells and its applications to typical internal micro-scale gas flows, including a micro-manifold, a micro-nozzle and a slider air bearing of computer hard disk, are described. This is aimed to further test the treatment of pressure boundaries by particle flux conservation; especially at subsonic speed, to gas flows involving many exits, more complicated geometry and moving boundaries. Firstly, results of a T-shaped micro-manifold with inlet Knudsen number of 0.2 show that excellent mass flow conservation between the inlet and two exits is obtained at low subsonic gas flows. Secondly, a micro-nozzle with the fixed inlet Knudsen number of 0.067 is simulated. For higher specified pressure ratio (exit to inlet), the location of maximum Mach number moves further downstream as the pressure ratio decreases; while, for lower specified pressure ratio, the Mach number increases all the way through the nozzle to the exit. Eventually, supersonic speed is observed at the exit for pressure ratio equal to or less than 0.143. Thirdly, for the gas flows of a slider air bearing of computer hard drive, the results agree very well with those of Alexander et al. (Phys. Fluids, 1994) for all the simulated conditions. In summary, the particle flux conservation concept has been proved successfully at multiple (more than two) pressure boundaries with complicated geometries and moving solid boundaries.