A numerical simulation that describes particle trajectories during chemical mechanical polishing by Zhao et al. was extended to account for the effects of larger particles in a slurry, particle location changes due to slurry dispensing and in-situ conditioning. Material removal rate (MRR) and within wafer non-uniformity were determined based on the calculated particle trajectory densities in the absence of chemical activity from the slurry and assuming that the pressure is uniform and constant. The effect of pad-wafer rotary dynamics and reciprocating motion of the wafer carrier on MRR uniformity were evaluated and typically edge-fast MRR profiles were obtained. It was also shown that in-situ conditioning improves the MRR uniformity of the polished wafers. Using the model, we also investigated the effect of particle size distribution and large particles (>200 nm in diameter) on wafer uniformity and scratch growth and compared with some of our wafer level defect data. It was shown that the presence of even 1 wt.% of larger particles can deteriorate the wafer uniformity.