Thermal embossing nanoimprint lithography (NIL) is an area of continuing interest because it allows direct patterning of nanoscale structures into a wide variety of functional polymer materials. Measuring the shape evolution of nanoimprinted lines during thermal annealing can provide insights into mechanisms of polymer stability and the dynamics of polymer flow. Recently, we have used optical scatterometry to extract the profile of nanoimprinted lines in low- and high-molecular mass polymer gratings during annealing of the gratings at the glass transition temperature. The data are obtained in situ using a spectroscopic ellipsometer and analyzed using a rigorous-coupled-wave scatterometry model. The results obtained from scatterometry are in very good agreement with those measured ex situ by atomic force microscopy and specular x-ray reflectivity, revealing very different decay mechanisms for gratings in low- and high-molecular mass polymers. The role of the selection of grating model in determining the uncertainties the grating line profile extracted from scatterometry is also discussed.© (2009) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.