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Building Information Modeling (BIM) covers the whole lifecycle of a building and facilitates the coordination of activities in the design, construction, and operation stages. However, during the design stages of pre-construction, it is time-consuming for a BIM project team to resolve design clashes as they integrate models finished by individual team members into a composite master model. To effectively overcome the issue, this study proposes a computer programming system. Based on the application programming interface provided by BIM software, a simulated annealing algorithm is employed to determine the layout modifications to minimize the number of design clashes. In this paper, the mechanical, electrical and plumbing (MEP) systems in a clean room on the first floor of an integrated circuit assembly factory are used to validate the effectiveness of the proposed system. The experimental results reveal the feasibility and effectiveness of the proposed system.