Micro/nano geometries with specified wall heat flux are widely encountered in electronic cooling and micro-/nano-fluidic sensors. In the present study we introduce a new iterative technique to impose a desired (positive/negative) wall heat flux boundary condition in the DSMC method that can be useful for simulation of Micro/Nano electro-mechanical systems (MEMS/NEMS) with given heat energy exchange. In the proposed algorithm we use the non-dimensional difference between computed and desired wall heat flux rates to improve iteratively an initial estimate of the wall temperature. A relaxation factor is applied to control the correction of wall temperature values. Effects of different numerical parameters such as number of simulator particles per cell and relaxation factor on the accuracy, performance and robustness of the iterative technique are investigated. We examine our iterative technique by analyzing heating and cooling processes in rarefied pressure-driven micro/nanoscale channel flows. Some unique behaviors are observed. For example, it is observed that contrary to the heating process, the cooling of micro/nano channel walls results in small variations in the density field. The upstream thermal creep effects in the cooling process decrease the velocity slip although the Knudsen number increases along the channel. Additionally, the cooling process changes the curvature of the pressure distribution making it below the linear incompressible one. For the cases considered here, our results indicate that flow cooling increases the mass flow rate through the channel, and vice versa. We also investigate the effects of wall heat transfer on the hydrodynamics and thermal behaviors of the 2-D micro/nano cavity flow.