A dual-wavelength microarray scanner based on laser confocal principle is constructed to detect two-color (Cy3/Cy5) fluorescence. Volume holographic filters are employed. It is not necessary to switch filters when samples tagged with Cy3 and Cy5 are scanned because of diffraction and band elimination property of volume holographic filter. Filter and gridding of microarray images based on order morphological methods are presented. Experimental result shows that sensitivity of the system is 0.1 fluo/μm2. The gridding algorithm is simple and effective.