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We propose an integration method of heterogeneous micro-electro-mechanical-system (MEMS) structures by liftoff and stamping transfer using a poly-(dimethylsiloxane) (PDMS) sheet. Silicon structures fabricated on multiple wafers were lifted off by PDMS sheets, and integrated onto a single wafer by the stamping transfer with high yield (>90%) and high accuracy (position error <500 nm). A two-dimensional (2D) integration and three-dimensional (3D) assembly of pyramid-like/inverted pyramid-like structures were demonstrated by our method. These demonstrations prove that our method enables us to integrate process-incompatible heterogeneous MEMS structures onto a single wafer.