We report a simple method to form metal-molecule-metal junctions (MMMs) via nanotransfer printing with low surface energy perfluoropolyether (PFPE) based stamps. Transfer printing is demonstrated onto thermally deposited metal thin film electrodes where the root-mean-squared roughness of these films is controlled by the deposition process and varies by 40% or more. Transfer of Au and Co thin films is reported onto Au/SAM and Co/SAM electrodes in well-ordered, 200 nm MMM arrays; furthermore, nickel nanotransfer printing is shown for the first time in the construction of 200 nm arrays of Ni/SAM/Ni junctions. The nanotransfer printing we report is reproducible in high fidelity which is required in the application of practical molecular electronic devices. Current-voltage characteristics are presented.