Nanoimprint lithography is conventionally used to transfer a pattern from a mold to a deformable and curable resist layer. Here we report a nanoimprinting technique to selectively transfer components of a pre- assembled nanostructure to a new substrate, while retaining the advantages of nanoimprint lithography such as low cost and high throughput. We use this technique to study metal particle roughness in Au ?nanofinger? substrates, along with the effects of annealing to reduce roughness, and the impact of annealing on the Surface Enhanced Raman Scattering (SERS) signal. The nanofinger substrates consist of Au-coated polymer pillars arranged to collapse into a designed assembly. Upon exposure to a volatile liquid and subsequent drying, microcapillary forces pull the pillars and their metal caps together into the designed structure. Successful transfer was achieved using the concept of template stripping via cold welding using a normal nanoimprinting process with no resist layer but under appropriate pressure to ensure even and complete transfer of all the nanostructures. Particle roughness was not found to be a significant factor in SERS from naonfinger substrates as annealing did not increase the observed Raman intensity.