In modern manufacturing environments, pollution management is critical as exposure to harmful substances can cause serious health issues. This study presents a two-stage computational fluid dynamic (CFD) model to estimate the distribution of pollutants in indoor production spaces. In the first stage, the Reynolds-averaged Navier–Stokes (RANS) method was used to simulate airflow and temperature. In the second stage, the Lagrangian method was applied for particle tracing. The model was applied to a theoretical acrylonitrile butadiene styrene (ABS) filament 3D printing process to evaluate the factors affecting the distribution of ultrafine particles (30 nm). Key parameters such as ventilation system effects, the presence of cooling fans and the print bed, and nozzle temperatures were considered. The results show that the highest flow velocities (1.97 × 10−6 m/s to 3.38 m/s) occur near the ventilation system’s inlet and outlet, accompanied by regions of high turbulent kinetic energy (0.66 m2/s2). These conditions promote dynamic airflow, facilitating particulate removal by reducing stagnant zones prone to pollutant buildup. The effect of cooling fans and thermal sources was investigated, showing limited contribution on particle removal. These findings emphasize the importance of digital twins for better worker safety and air quality in 3D printing environments.