The importance and applications of nanoscale magnetic storage devices has been of current interest owing to the extensive research interest in magnetic nanocaps. Continuing their research trend, we have attempted to synthesize and characterize an important isolated magnetic nanocaps system constituting Co and its oxide. CoO/Co thin films were deposited onto self-assembled arrays of polystyrene (PS) nanospheres (~600 nm diameter) under ultra-high vacuum environment using electron beam evaporation technique. The magnetic and structural properties of these nanostructures were then compared with those of simultaneously deposited films on bare Si substrate (referred to as reference film). The studied film and the reference film were grown in polycrystalline manner as observed from X-ray diffraction measurements while their roughnesses as observed from X- ray reflectivity were quite different. X- ray reflectivity showed that for the reference films well defined Kiessig oscillations appeared suggesting low roughness in the deposited films, while the films on PS followed the curvature of underlying nanospheres and thus have very high roughness resulting in the disappearance of Kiessig oscillations. Magnetic measurements exhibited a drastically high coercivity when the substrate was changed from flat (Si) to curved one (PS). As the film thickness was increased, the coercivity first showed a slight decrement (4.92 kA/m) and beyond 40 nm film thickness, it showed some enhancement (14.2 kA/m). The exchange bias measurements also showed interesting results with variation in film thickness. Co 10 nm film deposited on PS showed negative exchange bias of –127 kA/m which decreased to –26 kA/m in 100 nm film. The overall results were explained by correlating the magnetic and microstructural properties of the thin films as a function of thickness.