In a capillary electrophoresis separation performance is affected by various factors, for example, an electroosmotic flow, dispersion of sample plug and sample adsorption to capillary wall. In order to miniaturize the microcapillary onto a chip we have to understand them in detail and investigate their influence. Confocal Laser Scanning Microscopy (CLSM) in fluorescence mode (FV300 Fluoview OLYMPUS JAPAN CO., LTD, Japan) was used to observe the motion of the samples in microcapillary fabricated on a chip. The CLSM is a powerful tool to understand their influence since it can capture the fluorescence images sliced in the plane perpendicular to the optical axis and can scan the plane position along the optical axis. Therefore it makes possible to observe the sample behavior inside the channel. This study also contributes the investigation of the microfluidic manipulation which includes a micropump, a microvalve and other microfluidic actuator devices under electrokinetic driven conditions.