The non-equilibrium electro-thermodynamic properties of magnetized plasma produced by a modified radio-frequency magnetron sputtering system were investigated in detail. The plasma was analyzed using Hall, Langmuir, and Faraday probes and optical emission spectroscopy, and numerical simulations were conducted to determine the electric and magnetic field profiles. It is found that the occurrence of lower hybrid resonance and excitation of helicon waves are satisfied locally along the plasma profile (Z). This unusual effect in magnetron sputtering systems plays an important role in the increase of the electrons and ions temperature improving the quality of the films produced. Films of complex structure as hydroxyapatite that have biomedical applications were produced along the Z to confirm our plasma results. The films were characterized by performing grazing incidence X-ray diffraction using synchrotron radiation, X-ray photoelectron spectroscopy and atomic force microscopy. The microstructure analysis of hydroxyapatite films produced at different Z revealed that films with high crystallinities and with ideal stoichiometries (Ca/P = 1.67 ± 0.05) were produced within a magnetic cusp region (26 mm < Z < 32 mm). Based upon the results from plasma diagnostics and films characterization, we proposed a model of plasma of this system. The delivered energy by ions bombardment for films formation was determined and reached values around 8 eVs−1Å−2 and plasma temperature of T ≈ 10 eV inside the magnetic cusp region. Finally, this work opens the possibility to produce coatings of other complex compounds by the fine-tuning of resonant waves and their high delivered energies in vacuum magnetized plasmas.