The effect of swift heavy ion (SHI) irradiation on InGaAs/GaAs heterostructures is studied using Raman spectroscopy and atomic force microscopy (AFM). The structures consist of molecular beam epitaxy (MBE) grown InGaAs layers on GaAs(001), having layer thicknesses of 12, 36, 60 and 96 nm. After irradiation, the GaAs type longitudinal optical (LO) mode blue shifted to higher frequency in thin samples and red shifted towards lower frequency in thick samples. These results are discussed invoking the penetration depth of the probe radiation (λ = 514.5 nm) in InGaAs. Deconvoluting the Raman spectra of thin samples indicates a compressive strain developed in the substrate, close to the interface upon irradiation. This modification and diffusion of indium across the interface results in an increase of strain and reduction of the defect densities in the InGaAs layer. The variations in FWHM of the Raman modes are discussed in detail. The surface morphology of these heterostructures has been studied by AFM before and after SHI irradiation. These studies, combined with Raman results, help to identify different relaxation regimes.