An advanced multi-domain CFD analysis approach is proposed to calculate the scavenging flow process in motored two-stroke engines. An implicit and conservative treatment at the domain interface is developed which offers significant speedup in convergence. An arbitrary Lagrangian-Eulerian approach for moving grid and a grid remeshing technique for grid sliding at engine cylinder/transfer ports interfaces are used for efficiency and accuracy. A three-dimensional simulation of the Mercury Marine research two-stroke engine is carried out to demonstrate the approach. Six computational domains are used which naturally represent the geometries of the cylinder, engine dome, exhaust and transfer ports. The influence of boost port inclination angle on the scavenging process of the two-stroke engine is also studied numerically. The computation is supplemented with a standard two-equation turbulence model with compressibility correction. The calculated results show that the flow patterns vary rapidly with the piston motion. Complex non-uniform velocity distribution and vortical flows are developed in the engine cylinder and exhaust port. It is noticed that different arrangement of the boost port could alter the scavenging process significantly. In general, it is found that better scavenging efficiency is obtained with increasing boost angle.