Together with space-charge neutralization, ionization and charge exchange in the heavy ion beam fusion (HIBF) chamber can change beam quality and final focusing. Our research here supports simulation of these interactions through exploring theoretical approaches and developing improved models. This study is focused on the multi-electron processes which play an important role for these low-charged high-energy heavy ions. An improved classic trajectory Monte Carlo model and corresponding codes have been developed to simulate the heavy ion-atom collisions, which require intensive computations to solve many-body Hamiltonian Equations. Currently the results from the ion Xe^q+ (q = 1-18) colliding with Xe gas show that multi-electron effects are significant, and this cross section can reach about 40% of the total. The improved code is expected to be an integral part of a plasma simulation package designed to study the atomic effects in beam transport and focusing in HIBF using plasma neutralization techniques. This should help provide improved physical insight into current HIBF experiments and future studies.