In this work, complex 3D ferroelectric nanostructures on Poly(vinylidenefluoride-trifluoroethylene), P(VDF-TrFE), films have successfully been fabricated using a special hot-embossing process with two sequential shots on the same site with a grating template and a dot array template of the same periodicity at the same hot-embossing temperature. The nanostructures have been characterized with atomic force microscope (AFM), piezoresponse force microscope (PFM) and Fourier transformed infrared spectroscopy (FTIR). It is shown that sequential hot-embossing offers an effective way to fabricate complex 3D nanostructures of functional ferroelectric materials toward various applications.