We have fabricated Co-Pt nanodot arrays by electrochemical process for the application of bit patterned media (BPM), which is proposed as a key technology for future recording media. Since formation of uniform nanodot arrays is required for BPM, controlling the initial stages of electrodeposition is significant. In this work, we analyzed the effects of applied potential and size of nano-patterns on initial stages of Co-Pt electrodeposition. As a result, number of Co-Pt nuclei decreased in smaller nano-pore. In particular, formation of Co-Pt single grains, which exhibit high and uniform coercivity, was expected with low overpotential in nanopore with 10 nm diameter. Furthermore, coercivities of Co-Pt films at the initial stage increased with lower overpotential, since Co-Pt nucleated and grew along with Ru underlayer with high orientation. These results indicate that magnetic properties of Co-Pt nanodot arrays can be optimized by controlling the nucleation and growth behavior of Co-Pt.