CoPt films have been grown in the past with a high anisotropy in L11 or L10 phase, and a high coercivity is observed only in L10 CoPt films. Recently, we have grown CoPt films which exhibited a high coercivity without exhibiting an ordered phase. In this study, high resolution transmission electron microscopy (HRTEM) investigations have been carried out to understand the strong thickness and deposition pressure dependent magnetic properties. HRTEM studies revealed the formation of an initial growth layer in a metastable hexagonal (hcp) CoPt with high anisotropy. This phase is believed to be aided by the heteroepitaxial growth on Ru as well as the formation of Ru-doped CoPt phase. As the films grew thicker, transformation from hcp phase to an energetically favourable face-centered cubic (fcc) phase was observed. Stacking faults were found predominantly at the hcp-fcc transformation region of the CoPt film. The higher coercivity of thinner CoPt film is attributed to relatively less fcc fraction, less stacking faults, and to the isolated grain structure of these films compared to the thicker films.