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Swift heavy ion (SHI) beam mixing at metal/Si system forms various silicides at the interface. In the present study SHI induced mixing has been investigated at Si/Mn/Si interfaces using 120 MeVAu+9 ions at three different fluences of 1 × 1013, 5 × 1013 and 1 × 1014 ions/cm2. Specimens were characterized by Grazing Incidence X-Ray Diffraction (GIXRD), Atomic Force Microscopy (AFM), Rutherford Backscattering Spectroscopy (RBS) and Cross-sectional Transmission Electron Microscopy (XTEM) techniques before and after the irradiation. GIXRD results revealed the presence of Mn-silicide at the interface due to the atomic mixing after irradiation. AFM of the samples was used to determine surface roughness contribution to RBS. RBS and XTEM investigations confirmed Mn5Si2, MnSi and Mn4Si7 silicide phases at the interface.