Ion beam mixing is a useful technique to produce modifications at the surface and interface of the solid material. In the present work, ion beam induced modifications at Co/Si interface using 120 MeV Au-ion irradiation has been studied at ion fluences in the range of 10(12) to 10(14) ions/cm(2) by secondary ion mass spectroscopy (SIMS) technique and calculated mixing efficiency at the interface. Silicide formation has been discussed on the basis of swift heavy ion (SHI) irradiation induced effects. Surface morphology and roughness of irradiated system with fluence 5 x 10(13) and 1 x 10(14) ions/cm(2) is studied by scanning tunneling microscopy (STM). Roughness of the surface shows marks of melting process and confirms the appearance of some pinholes in the reacted Co/Si system. Comparative study was also undertaken on annealed sample at 300 degrees C and then irradiated at a dose 1 x 10(14) ions/cm(2). (c) 2006 Elsevier B.V. All rights reserved.