Successful fabrication of three-dimensional multilayer microstructures in thermoplastic polymers using optimized layer-transfer and transfer-bonding techniques are reported in this work. For successful multilayer fabrication, it is very important to control the adhesion between two polymer layers and between mold and polymer. The authors discuss two techniques, bonding with a thin adhesive layer and direct thermal bonding near glass transition temperature, to achieve good bonding between two polymer layers while maintaining the structural integrity of the bottom polymer layers. Bonding with an adhesive layer achieves near 100% yield and heterogeneous materials can be bonded by this method. Direct thermal bonding is a generic approach that is suitable for all thermoplastic polymers. It opens up the possibilities of creating 3D multilayer structures in functional polymers for advanced applications. The capability and flexibility of the techniques developed here are expected to have deep impact on the applications of soft materials such as polymers in micro- and nanofabricated devices and systems. (c) 2007 American Vacuum Society.