This study reports phonon confinement and strain effects in the Raman spectrum of ion-irradiated and subsequently etched α-quartz. Y- and Z-cut α-quartz single crystals were irradiated at room temperature with 20-MeV Ni6+ and 40-MeV I7+ ions. Latent ion tracks were produced with areal densities ranging from the isolated track regime to the overlapping track regime (nominal fluences of 1 × 109, 1 × 1010, and 1 × 1011 ions cm-2). Nanowell structures were revealed after vapor etching with hydrofluoric acid (HF) aqueous solutions. A phonon confinement model was invoked to explain the observed changes in the shape of the strong Raman peak located around 463 cm-1. Phonon coherence lengths of the irradiated samples were determined by fitting the confinement model to the experimental data. It was found that the phonon coherence lengths (L) decreased with increasing fluence (L ~ 66 nm for samples irradiated with 1 × 109 ions cm-2, L ~ 58 nm at 1 × 1010 ions cm-2, and L ~ 45 nm at 1 × 1011 ions cm-2), suggesting that ion tracks may confine optical phonons in quartz. An additional contribution to the upshift was observed at the highest fluence. This was attributed to a contribution from lattice strain when track separations are small and the overlapping strain fields around ion tracks extend through a large volume fraction of the crystal. Through an empirical correlation, the induced stress was estimated to be on the order of 100 MPa.