In this paper we show that BCB wafer bonding, combined with deep-reactive-ion-etching (DRIE) for silicon, and HF etching for FOTURAN glass are viable methods to fabricate three-dimensional microfluidics. The BCB film is patterned by dry-etching technique with a photoresist mask and the target wafer is then bulk-micromachined together with the BCB mask. The two micromachined wafers are then bonded together under vacuum or nitrogen gas environment, at low temperature. Silicon-glass, silicon-silicon and glass-glass are all possible bonding pairs using thermocompressive bonding with BCB. It was found that hard-cured BCB bonding is more suitable for microfluidic channel fabrications than soft-cured BCB bonding, due to adhesive overflows in microfluidic channels and delamination during wet etching.