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In this paper, we present a low-cost and rapid self-alignment process for temporary bonding of MEMS chip onto carrier wafer for size-free MEMS-IC integration. For the first time, a hydrophobic self-assembled monolayer (SAM), FDTS (CF3(CF2)7(CH2)2SiCl3), was successfully patterned by lift-off process on an oxidized silicon carrier wafer. Small volume of H2O (~μl/cm2) was then dropped and spread on the non-coated hydrophilic SiO2 surface for temporary bonding of MEMS chip. Our results demonstrated that the hydrophobic FDTS pattern on carrier wafer enables rapid and precise self-alignment of MEMS chip onto SiO2 binding-site by capillary force. After transfer the MEMS chips to target wafer, FDTS can be removed by O2 plasma treatment or UV irradiation.