We report (a) the deep modification of polymers by long-lived reactive species generated in atmospheric pressure plasma and (b) the dependence of plasma-polymer interaction on the macromolecular structure. Styrene-based polymers show significant thickness expansion whereas polymers with methyl, alcohol, and ether side groups show low-rate etching. The characterization of polystyrene (PS) by X-ray photoelectron spectroscopy and attenuated total reflectance-Fourier transform infrared shows that plasma treatment destroys aromatic rings and produces ether, ester, and surface organic nitrate groups.These modifications can happen at tens of nanometers below the surface, which we attribute to the reaction-diffusion of plasma species. Comparing three styrene-based polymers namely PS, poly(4methyl styrene), and poly(αmethyl styrene), we find that long-lived species primarily attack the C-H bond on the carbon site where the aromatic ring connects.