ZnS and ZnSe for infrared optical windows were fabricated by particular Chemical Vapor Deposition (CVD) process with so-called S method and Se method respectively. Their morphology and defects are reported in this paper. The microstructure, composition and the influence on optical properties of the defects were investigated. The process reasons leading to these defects were discussed as well. Hot isostatic pressing (HIP) treatment was adopted to eliminate some of the defects, and the effect of HIP on optical properties was evaluated.