The request of fluorescence microscopy filters was introduced. Optimized filter construction which requires more than 100 layers stack on both sides was redesigned. Surface deformation of filters caused by stress of multi-layers film was studied. The stress deformation effected by different film material and thickness was analyzed. A new flatten surface method was used to improve the surface flatness to 0.25λ. Filter sets were manufactured and photomicrograph was obtained with high contrast and no deformations when these filter sets were applied in fluorescence microscopy.© (2010) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.