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We have developed a robust, CMOS back end of the line (BEOL) compatible, wafer-scale device transfer, and interconnect method for batch fabricating systems on chip that are especially suitable for MEMS or VLSI-MEMS applications. We have applied this method to transfer arrays of 4096 free-standing cantilevers with good cantilever flatness control and high-density vertical electrical interconnects to the receiver wafer (typically CMOS). Such an array is used in a highly parallel, scanning-probe-based data-storage system, which we internally call "millipede." A very high-integration density has been achieved, even for wafer-scale transfer, thanks to the interlocking nature of the interconnect structure, which provides easy alignment with an accuracy of 2 μm. The typical integration density is 100 cantilevers/mm2 and 300 electrical interconnects/mm2. Note that only the cantilevers, not a chip with cantilevers, are transferred and, unlike flip-chip technology, our method preserves the device orientation, which is crucial for MEMS applications, where often the MEMS device should have access to its environment (in our case, the cantilever tips are in contact with the storage medium). After device transfer, the system is mechanically and electrically stable up to at least 500°C, allowing post-transfer wafer processing.