In a deposition system containing a planar planetary substrate holder, models for film thickness distribution without and with shadowing mask are developed. The shadowing mask optimized by numerical computation method is applied to achieve good thickness uniformity, while the deposition efficiency of the evaporated material is taken into consideration in the optimization. Experimentally, the theoretically designed shadowing mask is used to control the thickness distribution of the MgF2 coatings deposited by electron beam evaporation on a flat substrate with a planar planetary system. Uniformity measurements based on the reflection spectra of single layer MgF2 films demonstrate that uniformities is better than 99.6%, while the deposition efficiency of the evaporated material is higher than 87.4%.