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This paper demonstrates the design of a two dimensional nanoholes array opto-fluidic microscopy (OFM). Contrary to previous OFM designs, our design captures accurate real-time images of biological samples flowing in a microfluidic channel. In addition, the enhanced design allows us to monitor the flow of micro-organisms by continuously acquiring images with acceptable frame rate. Details of the enhanced OFM structure as well as the analysis that proves its feasibility and simulations that illustrates its advantages are all presented.