In-situ system for metallic multilayer thin films used for magnetic tunnel junction (MTJ) required a multi-target system to avoid the formation of impurities which make these devices very costly. In this work, the study was performed to resolve this issue by using a single target system for multilayer formation and impurity phases were dissolved by swift heavy ion (SHI) irradiation. A pristine MgO/Si(100) and CoFe2O4/MgO/ZnFe2O4/Si(100) (CFMZF) multilayer thin film were prepared via radio frequency (RF) sputtering technique. These structures were irradiated by 75 MeV oxygen-ion (O-ion) fluence (5x1011, 1x1012, and 5x1012 ions/cm2) and 200 MeV silver-ion (Ag-ion) fluence (1x1012 ions/cm2) for the investigation of structural changes. The high-resolution X-ray diffraction (HRXRD) reveals that MgO and CFMZF thin films have impurity peaks, dissolved via O-ion and Ag-ion irradiation. Further HRXRD analysis confirmed that Ag-ion irradiation dissolves more peaks leaving one small intensity peak of (400) corresponding to MgO. The multilayer stack of CFMZF irradiated via Ag-ion shows that Mg(OH)2 phase were completely dissolved and appears only (311) less intense peak corresponding to the ferrite structure. The findings are also corroborated by cross-sectional field emission scanning electron microscopy of CFMZF multilayer thin film showing damaged layers with Ag-ion irradiation. Therefore, the SHI irradiation technique can be used to dissolve the impurity peaks and improve the interface of the multilayer stacks.