A recently suggested technique for non-destructive investigation of inhomogeneities in thin objects, which is based on the measurement of the energy spectra of charged particles transmitted through the object, is used for the study of thermal annealing of 10–20 μm thick polyethylene terephtalate, polypropylene and polycarbonate foils irradiated with 1–10 MeV/amu heavy ions. At elevated temperature a foil linear contraction is observed on pristine and irradiated material. Also the foil roughness increases with increasing temperature. On the same foils with etched pores 0.5–1.0 μm in diameter, the thermal annealing results in gradual closing of the pores up to about 30% of their initial diameter at the temperatures of 150–175°C. At higher temperatures the pore diameter increases and achieves its initial value.