A method for continuous 3D visualization of the mold filling at a microscopic level during a thermoplastic nanoimprint process was developed. It is based on superposition of micrographs of a series of different stages of imprint. It was applied to two common 3D microscopies with different resolution limitations. Due to advanced image processing, the animated movie sequence, available as supplementary multimedia information in the online version of this journal, gives an unprecedented insight into the complex polymer flow and shows how voids are forming and vanishing during the imprint process around micropillars. The method has advantages over current real-time methods and can be used as an analytical tool for optimization of processes and improvement of stamp design down to the sub-10 nm nanometer range.