Development of innovative nano-bio-analytical systems is coming to reality by the combination of the microfluidic device technologies and the precise image processing systems using an optical microscope or a scanning probe microscope. Highly functional microfluidic devices can be fabricated by the application of advanced nano/microfabrication technologies developed in the ULSI industry. Microfluidic devices under development in our projects are expected to enable direct manipulation and analysis of each single cell and obtain molecular-level information about life phenomena of the cell, which has not been attainable by the conventional analysis tools. Recent progress and the future scope in plasma processing for microfluidic devices will be presented in this paper.