Thin membranes of PU and PEEK polymers were irradiated with 50MeV lithium ions for modifications in structural, optical and chemical properties. The XRD spectra indicated the alignment of polymeric chains in a regular pattern and hence there was decrease in the amorphous character of the irradiated polymers. The optical absorption of all irradiated samples shifted towards the visible region of the spectrum. It was attributed to the generation of a conjugated system of bonds which lowered the band gap energy of irradiated samples. The FTIR spectra obtained after irradiation exhibited decrease in absorbance for various bands in case of PU whereas PEEK showed minor changes in its chemical properties. The other results were discussed from the calculated parameters such as crystallite size, Urbach's energy and number of carbon hexagon rings per conjugation length from the analyses of the XRD and UV–visible data.