The surface morphology of polymers and polymer composites strongly influences both the adhesive bonding strength of composite structures and the electrical conduction through carbon fiber composites. Conventional surface modification techniques (such as mechanical abrading, chemical treatment, plasma treatment and flame treatment) not only damage the surfaces of polymers and polymer composites but also increase production cost. In this study, the surface of epoxy was modified by heating carbon black with electromagnetic waves in order to generate nanometer-sized grooves. A thermal transfer model was developed to investigate the generation mechanism of the grooves and the process variables. In the surface modification technique, electromagnetic waves and carbon black were used to improve both the bonding strength and the electrical conductivity of the composite in a fast and efficient way.