The localised surface plasmon resonance (LSPR) at the surface of metal nanostructures can induce a highly intense electromagnetic (EM) field, which is confined to the edges with big curvature or at narrow gaps between nanostructures. Therefore, the localisation of target molecules at these sites is crucial to achieve high sensitivity in LSPR-based biosensors. To this end, we fabricated a 40 nm high gold nano-truncated cone (GNTC) array using thermal nanoimprint lithography. As the EM field is most intense at the side surface and relatively weak at the top surface of GNTC, we improved the detection sensitivity by blocking the top surface with oxides to limit adsorption of antibodies and antigens to the top surface. We observed the difference in sensitivity by detecting α-fetoprotein (AFP) on the oxide-capped and uncapped GNTC arrays through sandwich immunoassay and enzymatic precipitation. The capped GNTC array exhibited higher detection sensitivity than the uncapped one. Particularly, six-fold enhancement of sensitivity was achieved in the serum sample. We used atomic force microscopy and electron microscopy to validate that the deposition of the oxides on the top surface of GNTC effectively blocked the adsorption of the biomolecules and the target molecules were preferentially adsorbed on the side surfaces.