The thin films of SiO2 and Si3N4 are deposited on the microstructure surface of a linear array mask by the techniques of photolithography, etching and plasma enhanced chemical vapor deposition (PECVD). The influences of the width and thickness of the linear array mask, as well as the film thickness and deposition rate on the reproducibility of SiO2 and Si3N4 films are investigated. A microstructure filter array with a good microstructure is prepared. The results show that the larger the film deposition rate is, the better the film reproducibility is. The increases of mask thickness and film deposition thickness lead to the deterioration of thin film reproducibility. The reproducibility of SiO2 films is better than that of Si3N4 films.