The controlled patterning of polymer resists by plasma plays an essential role in the fabrication of integrated circuits and nanostructures. As the dimensions of patterned structures continue to decrease, we require an atomistic understanding underlying the morphological changes that occur during plasma-polymer interactions. In this work, we investigated how plasma surface modifications and the initial polymer structure influenced plasma etch behavior and morphological changes in polymer resists. Using a prototypical argon discharge, we observed polymer modification by ions and vacuum ultraviolet (VUV) radiation from the plasma. A thin, highly dense modified layer was formed at the polymer surface due to ion bombardment. The thickness and physical properties of this ion-damaged layer was independent of polymer structure for the systems examined here. A relationship was observed that strongly suggests that buckling caused by ion-damaged layer formation on a polymer is the origin of roughness that develops during plasma etching. Our results indicate that with knowledge of the mechanical properties of the ion-damaged layer and the polymer being processed, plasma-induced surface roughness can be predicted and the surface morphology calculated. Examining a wide variety of polymer structures, the polymer poly(4-vinylpyridine) (P4VP) was observed to produce extremely smooth surfaces during high-ion energy plasma etching. Our data suggest that VUV crosslinking of P4VP below the ion-damaged layer may prevent wrinkling. We also studied another form of resists, silicon-containing polymers that form a SiO2 etch barrier layer during O2 plasma processing. In this study, we examined whether assisting SiO2 layer formation by adding Si-O bonds to the polymer structure would improve O2 etch behavior and reduce polymer surface roughness. Our results showed that while adding Si-O bonds decreased etch rates and silicon volatilization during O2 plasma exposure, the surface roughness became worse. Enhanced roughening was linked to the decrease in glass transition temperature and elastic modulus as Si-O bonds were added to the polymer structure. For polymers used as resists it is required that the mechanical properties of the ion-damaged layer and the polymer be taken into account to understand their roughening behavior.