The influence of transversal walls on a stationary near-isothermal gas flow in three dimensional microchannel configurations is studied using the Direct Simulation Monte Carlo (DSMC) method in the late slip regime and the transitional regime of the gas flow, for some selected values of the rarefaction parameter. The study was performed considering a straight, a 90 degree bend and a T-junction microchannels, with a rectangular cross-section. Implicit boundary conditions were utilized for applying a given pressure at the inlet and outlet boundaries. Some of the obtained results concern two dimensional configurations by confining the third dimension between two specularly reflecting walls, so that the flow in the third direction is homogeneous. A comparison of the DSMC produced results with those given by the finite volume based SIMPLE-TS was performed. The hard sphere model was used. The No Time Counter (NTC) scheme was used for computing the particle collisions. A DSMC based software was developed to study the gas flow in microchannel configurations, and a part of the results were obtained using an OpenMP parallel version of the software. (C) 2015 Elsevier Ltd. All rights reserved.