The effect of ion implantation (4 MeV12C2+, 5 MeV16O2+, and 8 MeV28Si2+) on [110] silicon wafers in channeling and random orientation is investigated by micro-Raman spectroscopy. The profiles were measured using Scanning Electron Microscope (SEM) showing that the ions were penetrating deeper inside the wafer in the channeling case creating a 1–2 µm wide strongly modified region and agreeing with the d-nuclear reaction analysis measurements. Micro-Raman spectroscopy was employed for the assessment of the lattice damage, probing the side surface of the cleaved wafers at submicron step. The phonon modifications show strong lattice distortions in zones parallel to the front surface of the wafers and at depths, which agree with the results of the characterization techniques. In these strongly damaged zones, there is a substantial reduction in the phonon intensity, a small shift in wavenumber position, and a large increase in the phonon width. On the basis of a modification of the phonon confinement model that takes under consideration the laser beam profile, the reduction in intensity of scattered light, and the nanocrystallite size distribution from the simulation of the lattice displacements, the main characteristics of the Raman spectra could be reproduced for the random C and O implantations. The results indicate that at a critical doping level, the induced defects and lattice distortions relax by breaking the silicon single crystal into nanocrystallites, thus creating the observed zones of strongly distorted lattice. Copyright © 2014 John Wiley & Sons, Ltd.