Defects were shown on the multiple cavity induced transmission filters (ITF),which greatly affected the sample′s quality and environmental stability. Four-cavity ITF were prepared by evaporation method on the float glass at room temperature. Defects topographies were observed by optical microscope,and the defects were divided into different kinds of dig defects and scratch defects. Depth information and elementary composition of defects were obtained by optical profiler and EDS energy spectra analysis. The results showed the defects were mainly caused by unclean substrate,sputtering and other composite reasons like stress and sub-surface defects. In order to suppress the defect with numbers,width and depth,acid cleaning techniques were tested and confirmed effective. Good results achieved with improved techniques were made according to genetic analysis of defects.