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Continuous crystallization of lipid nanoparticles, carrying bioactive compounds, is employed as a model system for food products to demonstrate benefits, application possibilities and challenges of microscale process engineering. It could be shown, that high and well-defined cooling rates (up to 104 times higher than standard batch processes) can be achieved by using a micro heat exchanger device for the continuous melt crystallization of lipid nanoparticles distributed in an emulsion, resulting in well-defined product qualities. Several formulations led to fouling and blocking of small passages in the micro heat exchanger. Fouling, blocking and associated challenging cleaning issues are often drawbacks for the use of micro devices for particulate flows in industry applications. Furthermore, no standardized design methods for cleaning strategies exist for microstructured devices. This contribution addresses the design of cleaning strategies for microstructured devices, demonstrated using a model process. The design of the cleaning strategies at the micro scale is realized with standardized macroscopic methods, namely fluid dynamic gauging and a simple flow channel. Analogies and differences between cleaning macro and micro devices are discussed.