Electromagnetic heating such as microwave processing has evolved as a promising technique to bond polymer substrates due to its ability to achieve non-contact, selective heating and localized melting. In microwave assisted bonding process, two polymer layers such as PMMA (polymethyl methacrylate) substrates can be bonded by heating a thin layer of dielectric material placed between the polymer layers. To better understand the bonding process of polymer layers, a detailed theoretical analysis has been presented. In this analysis, the bonding process of polymer substrates has been modeled as a multilayered composite slab exposed to microwave radiations. The electric field distribution along each layer is computed from simplified Maxwell's equation under plane wave configuration, and the Poynting theorem is used to find the volumetric power absorbed by each layer. The absorbed power is then used as the source term in unsteady energy equation which is solved by linear decomposition and separation of variables techniques. Finally, the closed form analytical solution obtained from this analysis is used to study the effect of material properties on temperature distribution of polymer substrate (PMMA) with poly-aniline as intermediate sacrificial layer. The analysis was carried out at household microwave frequency (2.4 GHz) with temperature dependent dielectric properties for both poly-aniline and PMMA layers. Our results show that dielectric properties, layer thickness, heat transfer coefficient and processing time have significant influence on the heating pattern. Results also show that the temperature of the PMMA substrate remains below the melting point globally, except at the interface of the poly-aniline layer due to its transparent nature to incident microwave radiation at 2.4 GHz. (C) 2012 Elsevier Ltd. All rights reserved.