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Novel nano microfluidic systems hold the potential to be used for innovative biomedical applications such as the encapsulation of single cells. Droplet-based microfluidic systems are able to resolve precisely biological processes running in small droplets according to their reaction time and place. High throughput analysis of biological substances such as cells can be achieved with droplet-based systems due to the serial flow of the droplets. One challenge so far is the fabrication of low cost microfluidic systems which are able to generate droplets at stable high rates and with a constant droplet volume. One approach to this problem is the fabrication of microfluidic systems with super hydrophobic channel walls so that a periodic droplet break up with a constant volume is ensured. This assumption was indicated by the results of simulations performed with channel systems having super hydrophobic and hydrophilic surface properties. Hence, we present a novel fabrication method to create microfluidic systems with tubular channel walls having super hydrophobic surface properties realised by a combination of hot embossing and thermoforming. Experiments were conducted with surface modified and unmodified microfluidic systems. The results obtained during the experiments verified the simulation assumptions: a periodic droplet break up with a constant droplet volume could be observed with microfluidic channel systems having super hydrophobic surface properties and an unstable droplet break up leading to different droplet volumes could be observed with the unmodified systems. These novel nano microsystems furthermore allow the design and cheap fabrication of biocompatible systems with several different thermoplastic polymers which makes this fabrication method highly flexible.