A combination of XPS, reflectance infrared spectroscopy, and neutron reflectivity measurements has been used to probe the spatial and global extents to which carboxylic acid motifs in electrodeposited conducting polymer films can be functionalized by reaction with vapor phase reagents (a carbodiimide together with trifluoroethanol) with the goal of controlling hydrophobicity. Across a range of polymer deposition and reaction temperatures, neutron reflectivity showed that, surprisingly, functionalization of the polymer matrix at depths > 5-10 nm into the polymer film was always significantly lower than at the exposed surface. The most efficient functionalization was found to occur when a low-density polymer matrix was prepared by elution of motifs cleaved from the polymer by base hydrolysis. Finally, when trifluoroethanol functionalization was performed, the macroscopic property of hydrophobicity was related to the surface, internal microstructure, and composition of the reacted films as elucidated by the above combination of probes.