Polymer based microfluidic devices have an important potential use in BioMEMs applications due to the low cost and biocompatibility. However, sealing the devices hermetically without blocking the channels, altering their dimensions or changing the surface properties is a challenging issue in their fabrication. In this paper a microwave-based sealing technique using a polymethylmethacrylate (PMMA) substrate and conductive polymer (polyaniline) is presented. The developed novel bonding technique has achieved precise, well-controlled and selective heating, which causes localized melting of the polymer substrates. At the joint interface, patterned polyaniline features absorb electromagnetic radiation and convert it into heat, which facilitates the microwave bonding of two PMMA substrates. This new approach can easily seal microfluidic devices with micron-sized channels without blocking or destroying the integrity of the channel. Microfluidic channels of 400 μm and 200 μm wide were sealed using a microwave power of 300 Watts, in less than 20 seconds. The microfluidic channel fabrication techniques, polyaniline patterning method at the interface and bonding evaluation such as sample cross section and leak test are discussed. The dielectric properties of polyaniline and PMMA at 2.45 GHz frequency are also evaluated by using the open probe technique, which shows PMMA is essentially transparent to microwave energy.