Among soft lithography techniques, Thermal Nanoimprint Lithography (NIL) is a high-throughput and low-cost process that can be applied to a broad range of thermoplastic materials. By simply applying the appropriate pressure and temperature combination, it is possible to transfer a pattern from a mold surface to the chosen material. Usually, high-resolution and large-area NIL molds are difficult to fabricate and expensive. Furthermore, they are typically made of silicon or other hard materials such as nickel or quartz for preserving their functionality. Nonetheless, after a large number of imprinting cycles, they undergo degradation and become unusable. In this paper, we introduce and characterize an innovative two-step NIL process based on the use of a perfluoropolyether (PFPE) intermediate mold to replicate sub-100 nm features from a silicon mold to the final thermoplastic material. We compare PFPE elastomeric molds with molds made of the standard polydimethylsiloxane (PDMS) elastomer, which demonstrates better resolution and fidelity of the replica process. By using PFPE intermediate molds, the nanostructured masters are preserved and the throughput of the process is significantly enhanced.