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Although apodization patterns have been adopted for the analysis of sputtering sources, the analytical solutions for the film thickness equations are yet limited to only simple conditions. Empirical formulations for thin film sputtering lacking the flexibility in dealing with multi-substrate conditions, a suitable cost-effective procedure is required to estimate the film thickness distribution. This study reports a cross-discipline simulation program, which is based on discrete particle Monte-Carlo methods and has been successfully applied to a non-imaging design to solve problems associated with sputtering uniformity. Robustness of the present method is first proved by comparing it with a typical analytical solution. Further, this report also investigates the overall all effects cause by the sizes of the deposited substrate, such that the determination of the distance between the target surface and the apodization index can be complete. This verifies the capability of the proposed method for solving the sputtering film thickness problems. The benefit is that an optical thin film engineer can, using the same optical software, design a specific optical component and consider the possible coating qualities with thickness tolerance, during the design stage.