Structural and magnetic properties of Ni magnetic nanocaps synthesized using electron beam evaporation technique under ultra high vacuum conditions are presented for two Ni layer thicknesses, namely 10 nm and 20 nm. To prepare them, Si (100) substrate was first drop coated with soft polystyrene (PS) nanopheres with the average diameter of 800 nm followed by the evaporation of Ni onto dried substrate. For the comparative analysis, the films were simultaneously deposited on plane Si substrate. The films were characterized for their crystalline properties using X-ray diffraction measurement in grazing incidence geometry, while other structural properties such as roughness and thickness of these films were extracted from the fitting of X-ray reflectivity data. The parameters were then correlated with the magnetism observed in these films using magneto-optical Kerr effect (MOKE) technique. The influence of thickness in these properties is discussed here.