In order to control nanoimprint lithography (NIL) processes for achieving good fidelity, the fast, low-cost, non-destructive and accurate measurement of geometric parameters of templates and imprinted grating structures is of great importance. Compared with conventional ellipsometric scatterometry, which only obtains two ellipsometric angles and has 2 changeable measurement conditions, i.e., the wavelength and the incidence angle, Mueller matrix ellipsometry (MME) can provide up to 16 quantities of a 4×4 Mueller matrix in each measurement with 3 changeable measurement conditions, i.e., the wavelength, the incidence angle and the azimuthal angle. Therefore, MME can acquire much more useful information about the sample. It is expected that much more accurate measurements of nanostructures can be achieved by choosing proper measurement configurations and completely using the rich information hidden in the measured Mueller matrices. Accordingly, the templates and imprinted grating structures in NIL processes are measured using an in-house developed Mueller matrix ellipsometer. We experimentally demonstrate that more accurate quantification of geometric parameters, such as line width, line height, sidewall angle and residual layer thickness, can be achieved by performing MME measurements in the optimal configuration and meanwhile by incorporating depolarization effects into the optical model. Moreover, as for the imprinted grating structures, the residual layer thickness variation over the illumination spot can also be directly determined by MME. The comparison between MME-extracted template and imprinted resist profiles also indicates an excellent fidelity of the nanoimprint pattern transfer process.