While nanotechnology was originally limited to small areas of a few cm2, the quest for lower costs has been the latest years the drive for developing processes utilising larger substrate sizes at increasing throughputs. A typical example is the flat panel display industry where the push to larger gen size and faster processing has resulted in a significant cost reduction. The next challenge here is the move to smaller feature sizes. Large area processing at high speeds is optimal when using roll-to-roll (R2R) processing, able to deliver the ultimate cost reduction. Flexible innovative thin film devices, like organic light emitting diodes (OLEDs) for lighting, photo voltaic (PV) and organic photo voltaic (OPV) modules, organic circuitry, printed electronics and thin film batteries, are currently developed using this kind of processing.The overall objective of Clean4Yield is the development and demonstration of technologies and tools for nano-scale detection, cleaning, prevention and repair of defects and contaminations in nano-scale layers. The R2R production processes for OLED, OPV, and high-end moisture barrier layers on flexible substrates will serve as development platform for the various methods. Clean4Yield will demonstrate that the developed methods increase yield, reduce production costs, and improve performance and operational device lifetimes of these applications. The developed technologies will be easy to adapted for other large-scale production technologies of other nano layer applications.