Molecular dynamics simulations are used to investigate the plastic deformation behavior of Cu50Zr50/Cu amorphous/crystalline (A/C) multilayered nanofilms with different interface directions, number of layers and temperatures under the imprinting process. The results show that the loading force of multilayered nanofilms grows with increasing thickness of layers and decreasing temperature. Specifically, the maximum stress is larger with increasing layer thickness, this shows an inverse Hall-Petch relationship between the stress and the layer thickness. The local stress is focused around the stamp and rises up as increasing imprinting depth. The plastic deformation behaviors are realized by dislocations or stacking faults in crystalline layers and shear transformation zones (STZs) or shear bands in amorphous layers. Additionally, the propagation of shear bands or spatial correlation of STZs in an amorphous layer can be disrupted at the amorphous/crystalline interfaces (ACIs). The centrosymmetry parameter (CSP) and dislocation analysis (DXA) reveal the nucleation of stacking faults at the ACIs and the Shockley partial dislocation account for 80% in the total dislocations in all cases. The affected region extends and displacement of atoms becomes more irregular as increasing temperature. Besides, the radial distribution function (RDF) reveals the structure of the material is more stable at low temperature. The transverse interface specimens and thinner layer thickness, and high temperature are facilitated to material formability.