The purpose of this paper is to investigate both theoretically and experimentally how nanocavities are replicated in the injection moulding manufacturing process. The objective is to obtain a methodology for efficiently replicate nanocavities. From the theoretical point of view, simulations are carried out using a submodeling approach combining Solidworks Plastics for a first macrosimulation and Fluent solver for a subsequent nanosimulation. The effect of the four main factors (melt temperature, mould temperature, filling time and cavity geometry) are quantified using an statistical 2 factorial experiment. It is found that the main effects are the cavity length, the mould temperature and the polymer temperature, with standardized effects of 5, 3 and 2.6, respectively. Filling time has a negative 1.3 standardized effect. From the experimental point of view, Focused Ion Beam technique is used for mechanizing nanocavities in a steel mould. The replication achieved in polycarbonate injection is quantified using an Atomic Force Microscope. It is observed how both the geometry and the position of the cavities in the mould affect its replication.