The main challenges in the manufacture of composite materials are low surface energy and the presence of silicon-containing contaminants, both of which greatly reduce surface adhesive strength. In this study, carbon fiber (CF) and E-glass epoxy resin composites were surface treated with the Accelerated Thermo-molecular adhesion Process (ATmaP). ATmaP is a multiaction surface treatment process where tailored nitrogen and oxygen functionalities are generated on the surface of the sample through the vaporization and atomization of n-methylpyrrolidone solution, injected via specially designed flame-treatment equipment. The treated surfaces of the polymer composites were analyzed using XPS, time of flight secondary ion mass spectrometry (ToF-SIMS), contact angle (CA) analysis and direct adhesion measurements. ATmaP treatment increased the surface concentration of polar functional groups while reducing surface contamination, resulting in increased adhesion strength. XPS and ToF-SIMS showed a significant decrease in silicon-containing species on the surface after ATmaP treatment. E-glass composite showed higher adhesion strength than CF composite, correlating with higher surface energy, higher concentrations of nitrogen and CO functional groups (from XPS) and higher concentrations of oxygen and nitrogen-containing functional groups (particularly C2H3O+ and C2H5NO+ molecular ions, from ToF-SIMS). Copyright © 2010 John Wiley & Sons, Ltd.