The thermal embossing form of nanoimprint lithography is used to pattern arrays of nanostructures into three different polymer films. The shape of the imprinted patterns is characterized with nanometer precision using both x-ray scattering and reflectivity techniques. The time dependent response of the pattern shape at temperatures near the glass transition temperature reveals large levels of residual stress induced by the imprinting process. During the imprint, large shear fields are generated as the viscous polymer flows into the mold. If these shear distortions do not have time to relax during the imprinting, internal stresses are frozen into the final pattern. At elevated temperatures in the freestanding structures (once the mold has been separated from the imprint), there is an accelerated reduction in pattern height in the reverse direction from which the material originally flowed into the mold. Factors that influence this residual stress include the relative molecular mass or viscosity of the resist and the amount of time the pattern is annealed at high temperature in the presence of the mold. (c) 2006 American Vacuum Society.