This study describes the development of a high throughput purification process of nucleic acid using amino-functionalized silica coated ferrite nanoparticles. The magnetic ferrite nanoparticles were synthesized and coated by a silica precursor in controlling the coating thicknesses and sizeses. The surface modification was performed with amino-functionalized organic silanes on silica coated magnetic nanoparticles. The spectroscopic measurements such as a FT-IR (ATR-method) and Vibrational Sample Magnetometer (VSM) were used to characterize the chemical structures and magnetic strengths. To elucidate the relationship between surface area, pore size distribution and reactivity of the materials, BET and Zeta potential were used. The use of functionalized self-assembled magnetic ferrite nanoparticles for a nucleic acid separation process provides a lot of advantages compared to the conventional silica based process.