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 C O functional groups (from XPS) and higher concentrations of oxygen and nitrogen-containing functional groups (particularly C 2 H 3 O + and C 2 H 5 NO + molecular ions, from ToF-SIMS).