We have studied ion-induced effects in the near-surface region of two eutectic systems. Gold and Silver nanodots on Silicon (100) substrate were prepared by thermal evaporation under high vacuum condition at room temperature (RT) and irradiated with 1.5 MeV Au2+ ions at flux ~1.25 x 10(11) ions cm-2 s-1 also at RT. These samples were characterized using cross-sectional transmission electron microscopy (XTEM) and associated techniques. We have observed that gold act as catalysis in the recrystallization process of ion-beam-induced amorphous Si at room temperature and also large mass transport up to a distance of about 60 nm into the substrate. Mass transport is much beyond the size (~ 6-20 nm) of these Au nanodots. Ag nanoparticles with diameter 15-45 nm are half-way embedded into the Si substrate and does not stimulate in recrystallization. In case of Au nanoparticles upon ion irradiation, mixed phase formed only when the local composition and transient temperature during irradiation is sufficient to cause mixing in accordance with the Au-Si stable phase diagram. Spectroscopic imaging in the scanning TEM using spatially resolved electron energy loss spectroscopy provides one of the few ways to measure the real-space nanoscale mixing.