Microfluidics deals with the behavior, precise control and manipulation of fluids at a micro scale. It has become increasingly prevalent in various applications such as biomedical applications (diagnostics, therapeutics, and cell/tissue engineering), inkjet head, and fuel cells etc. The issue of inspection and characterization of microfluidics has emerged as a major consideration in design, fabrication, and detection of microfluidic devices. In this paper, we characterize a diffusion based mixing in Y-microchannel using a fluorescent optical scanner based on a DVD pick-up module, which is widely used in optical storages. Using fluorescent dye, we measure the fluorescent intensity that represents the mixing patterns in Y-microchannel. We also compare these experimental results with computational fluid dynamics (CFD) simulation ones. It is shown that the proposed optical scanner can be used as an alternative measurement system with high performance and cost-effectiveness, compared to conventional optical tools such as epifluorescent microscopes using high resolution CCD camera and confocal microscopes with photomultiplier (PMT) detectors.