The origin and nature of instabilities in ultrathin resist (UTR) polymer films (less than or equal to 100 nm) spin coated onto silicon wafer substrates are presented, along with the influence of the substrate on the morphological, thermophysical, and viscoelastic properties of the polymers. The defects, morphology, and density of UTR films spin coated from well-characterized and commercially available phenolic ESCAP polymer based XP-98248 resist from Shipley which were annealed below the glass transition temperature are presented as a function of film thickness and spin coating parameters. For each firn, three distinct layers with different densities and varying degrees of roughness are observed: a surface layer, a bulk layer, and a substrate/film interface layer. The thickness of the surface layer is comparable to length scales of cooperative dynamics in polystyrene chains. Dependence of the density and roughness on total film thickness is observed for each layer, with the film/substrate interface layer showing the most variation for film thickness <53 nm, suggesting the onset of instabilities due to interfacial effects, polymer chain packing constraints, and cooperative dynamics. Within the thickness range of 65-100 nm, no dependence of defectivity on total film thickness and spin speed is observed. F-2 (157 nm) laser imaging results obtained on these films are discussed. Significant differences between UTR films (60 nm) and thick resist films (>400 nm) imaging performance are observed. An explanation is given in terms of polymer cooperative dynamics and interfacial effects.