Evolution of the structure and surface morphology of thin films composed of two selenium based chalcogenide phases, AgInSe2 and Ag2Se on 140 MeV ion irradiation is reported. At this high energy, the projectile Ni ions sputtered the surface of the films through energy deposition to the target electrons. The sputtering led to decrease of silver and selenium concentration, but did not affect indium concentration. Surface analysis by field emission scanning electron microscopy study revealed nanoparticles of widely varying shapes and sizes on the surface of the films. Irradiation did not affect the particle size distribution which peaked at similar to 100 nm. The two phases, AgInSe2 and Ag2Se exhibited different sensitivity to 140 MeV Ni ion irradiations. While Ag 2 Se phase was insensitive, the AgInSe2 phase showed complex structural modifications at intermediate fluences, finally getting amorphized at high ion fluences. Analysis of the fluence dependence of Grazing Incidence X-ray Diffraction (GIXRD) peak area of AgInSe2 phase indicated that each ion that penetrated the film, created an amorphous column of 1.6 nm radius. Surrounding the amorphous column, a cylindrical crystalline AgInSe2 region of radius 8.2 nm, but with reduced lattice parameters formed. High resolution transmission electron microscopy image also confirmed registration of amorphized tracks and the modified crystalline region of similar radii around the path of 140 MeV Ni ions in a grain of AgInSe2 as obtained from GIXRD study.