This paper presents the visualization method in which 3-dimensional(3D) microchannel flow can be detected using a confocal scanning microscope. By soft-lithography, we fabricated various Bio-MEMS(Micro Electro-Mechanical System) devices such as a disposable microchip for a flow cytometer and a micro-mixer, which have 3D structures. Injecting aqueous fluorescent solution in the microfluidic devices, we measured the flow in a steady state by the confocal scanning microscope. At first, we explain the principle of the confocal scanning microscope. And then we show the results from 3D visualization of microscopic flow structures using the confocal scanning microscope.