In the present work, a complete algorithm is presented to simulate the gas exchange process across domains in a multi-block computation involving a piston-controlled port. The moving boundary scheme of Peric is used in conjunction with the zonal boundary scheme of Rai. The algorithm has been applied to two cases. The first case involves a typical air-filling process through the piston-operated port of a pneumatic pump, and the analysis shows that flowfield variable information is smoothly communicated across the zonal boundary using this algorithm. The second case involves modelling of the scavenging process in a loop-scavenged two-stroke internal combustion (IC) engine. In this case, the stepwise evolution of the scavenging flow in the engine cylinder is studied. Initiation of short circuiting at early stages of scavenging, tilting of the inlet flow in directions different from inlet port angles and the existence of a low-purity swirling loop in the exhaust-side top corner of the engine cylinder are observed from the flowfield computations.