Thin silicon chips with a thickness of 50 μm are of light weight and are able to swim on droplets of fluids like for instance water. If the liquid shows a specific wetting behavior with respect to the underlying substrate then droplet and chip can move and self-align. Recent research work was carried out to determine the self-alignment accuracy of 50 μm thin silicon dies on plasma programmed surfaces. The self-alignment process sequence for die assembly comprise the following steps: surface programming by CF4 plasma treatment, dispense droplets of water on the metal target areas, pick-up of a 50 μm thin chip, move chip tool above the selected target area, let the chip fall down and self-align on the liquid surface on the target area. Within short time the droplet dries off and then the thin die sticks to the substrate. Self-alignment accuracy was measured by infrared microscopy at the position of the alignment marks of top and bottom devices. The paper will report in detail about sample preparation, selective plasma programming, self-alignment accuracy of thin dies and its dependence of the die size. Furthermore, the chemical composition of the relevant surfaces after CF4 plasma activation were analysed by XPS measurements.