In this work we present controlled, low-damage nanotopographic surface modification of poly(ethylene terephthalate) (PET). High-resolution nanopatterning over macroscopic areas was performed by "low-temperature" hot embossing lithography (HEL). While for standard HEL the temperature is typically raised up to many tens of Celsius degrees above the polymer glass transition temperature (T-g), we demonstrate optimal results at a temperature very close to the bulk T-g of PET (72 degrees C). Nanopits and nanobarcodes were transferred onto the surface of PET commercial sheets, demonstrating reliable sub-100 nm resolution over macroscopic areas. Sample optical, mechanical, and thermal characteristics were systematically analyzed before and after embossing at low (75 degrees C) and high (150 degrees C) temperature by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, tensile tests, and differential scanning calorimetry (DSC). We show that, while conventional high-temperature HEL can lead to dramatic degradation of the polymer in terms of transparency, flexibility, and crystallinity content, our low-temperature process fully maintains original surface and bulk substrate properties.