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The flow properties and substrate deposition rate profile, which are the important parameters in electron beam physical vapor deposition, are investigated computationally in this article. Collimators are used to achieve the desired vapor beam and deposition rate profile in some applications. This increases the difficulty measuring boundary conditions and the size of the liquid metal pool inside the collimators. It is accordingly hard to obtain accurate results from numerical calculations. In this article, two-dimensional direct simulation Monte Carlo (DSMC) codes are executed to quantify the influence of uncertainties of boundary conditions and pool sizes. Then, three-dimensional DSMC simulations are established to simulate cerium and neodymium evaporation with the collimator. Experimental and computational results of substrate deposition rate profile are in excellent agreement at various evaporation rates and substrate heights. The results show that the DSMC method can assist in metal evaporation with a collimator.