The differences in labeling efficiency and excited energy between two fluorescent dyes(Cy3,Cy5),gains and dynamic range between red and green channels result in the systematic variation in dual-wavelength microarray scanning.A normalization method with order morphology filter is presented.The background estimations of each spot are done by percentile filtering after fluorescent micoarray gridding which is employed by minimum filtering.The result shows that the ratio of two-color fluorescent intensity could be corrected appropriately.