In order to control nanoimprint lithography processes to achieve good fidelity, accurate characterization of structural parameters of nanoimprinted resist patterns is highly desirable. Among the possible techniques, optical scatterometry is relatively ideal due to its high throughput, low cost, and minimal sample damage. Compared with conventional optical scatterometry, which is usually based on reflectometry and ellipsometry and obtains at most two ellipsometric angles, Mueller matrix ellipsometry (MME) based scatterometry can provide up to 16 quantities of a 4 × 4 Mueller matrix in each measurement and can thereby acquire much more useful information about the sample. In addition, MME has different measurement accuracy in different measurement configurations. It is expected that much more accurate characterization of nanoimprinted resist patterns can be achieved by choosing appropriate measurement configurations and fully using the rich information hidden in the measured Mueller matrices. Accordingly, nanoimprinted resist patterns were characterized using an in-house developed Mueller matrix ellipsometer in this work. We have experimentally demonstrated that not only more accurate quantification of line width, line height, sidewall angle, and residual layer thickness of nanoimprinted resist patterns can be achieved, but also the residual layer thickness variation over the illumination spot can be directly determined, when performing MME measurements in the optimal configuration and meanwhile incorporating depolarization effects into the optical model. The comparison of MME-extracted imprinted resist profiles has also indicated excellent imprint pattern fidelity.