Photolithographic patterning of organic materials and plasma-based transfer of photoresist patterns into other materials have been remarkably successful in enabling the production of nanometer scale devices in various industries. These processes involve exposure of highly sensitive polymeric nanostructures to energetic particle fluxes that can greatly alter surface and near-surface properties of polymers. The extension of lithographic approaches to nanoscale technology also increasingly involves organic mask patterns produced using soft lithography, block copolymer self-assembly, and extreme ultraviolet lithographic techniques. In each case, an organic film-based image is produced, which is subsequently transferred by plasma etching techniques into underlying films/substrates to produce nanoscale materials templates. The demand for nanometer scale resolution of image transfer protocols requires understanding and control of plasma/organic mask interactions to a degree that has not been achieved. For manufacturing of below 30 nm scale devices, controlling introduction of surface and line edge roughness in organic mask features has become a key challenge. In this article, the authors examine published observations and the scientific understanding that is available in the literature, on factors that control etching resistance and stability of resist templates in plasma etching environments. The survey of the available literature highlights that while overall resist composition can provide a first estimate of etching resistance in a plasma etch environment, the molecular structure for the resist polymer plays a critical role in changes of the morphology of resist patterns, i.e., introduction of surface roughness. Our own recent results are consistent with literature data that transfer of resist surface roughness into the resist sidewalls followed by roughness extension into feature sidewalls during plasma etch is a formation mechanism of rough sidewalls. The authors next summarize the results of studies on chemical and morphological changes induced in selected model polymers and advanced photoresist materials as a result of interaction with fluorocarbon/Ar plasma, and combinations of energetic ion beam/vacuum ultraviolet (UV) irradiation in an ultrahigh vacuum system, which are aimed at the fundamental origins of polymer surface roughness, and on establishing the respective roles of (a) polymer structure/chemistry and (b) plasma-process parameters on the consequences of the plasma-polymer interactions. Plasma induced resist polymer modifications include formation of a thin (∼1–3 nm) dense graphitic layer at the polymer surface due to ion bombardment and deeper-lying modifications produced by plasma-generated vacuum ultraviolet (VUV) irradiation. The relative importance of the latter depends strongly on initial polymer structure, whereas the ion bombardment induced modified layers are similar for various hydrocarbon polymers. The formation of surface roughness is found to be highly polymer structure specific. Beam studies have revealed a strong ion/UV synergistic effect where the polymer modifications introduced at various depths by ions or ultraviolet/UV photons can interact. A possible fundamental mechanism of initial plasma-induced polymer surface roughness formation has been proposed by Bruce et al. [J. Appl. Phys. 107, 084310 (2010)]. In their work, they measured properties of the ion-modified surface layer formed on polystyrene (PS) polymer surfaces, and by considering the properties of the undamaged PS underlayer, they were able to evaluate the stressed bilayer using elastic buckling theory. Their approach was remarkably successful in reproducing the wavelength and amplitude of measured surface roughness introduced for various ion bombardment conditions, and other variations of experimental parameters. Polymer material-dependent VUV modifications introduced to a depth of about 100 nm can either soften (scission) or stiffen (cross-linking) this region, which produce enhanced or reduced surface roughness.