As part of a study on the deposition of superconducting films of YBa2Cu3O7-delta a three-dimensional electron beam physical vapor deposition process of yttrium in a vacuum chamber is investigated both computationally and experimentally. The numerical analysis employs the direct simulation Monte Carlo (DSMC) method. The experimental studies consist of atomic absorption spectra taken in the evaporated yttrium plume and deposited film thickness profiles. Some important modeling issues such as atomic collision cross sections for metal vapors and hyperfine electronic structure of the atomic absorption spectra are addressed. Film deposition thicknesses on the substrate and atomic absorption spectra given by the DSMC method and experiment are in excellent agreement. Collisions between the atoms are found to have a significant effect on the film growth rate and area of uniform deposition as the evaporation rate of yttrium increases.