We present the fabrication and optical characterization of plasmonic nanostructures consisting of nanohole arrays in two thin films, a metal and a dielectric. A novel method called mask-on-metal colloidal lithography is used to prepare high aspect ratio holes, providing efficient mass fabrication of stable structures with close to vertical walls and without the need for an adhesion layer under the metal. Our approach for understanding the transmission properties is based on solving the dispersions of the guided modes supported by the two films and calculating the influence from interference. The methodology is generic and can be extended to multilayered films. In particular, the influence from coupling to waveguide modes is discussed. We show that by rational design of structural dimensions it is possible to study only bonding surface plasmons and the associated hole transmission maximum. Further, numerical simulations with the multiple multipole program provide good agreement with experimental data and enable visualization of the asymmetric near-field distribution in the nanohole arrays, which is focused to the interior of the "nanowells". The refractometric sensitivity is evaluated experimentally both by liquid bulk changes and surface adsorption. We demonstrate how the localized mode provides reasonably good sensitivity in terms of resonance shift to molecular binding inside the voids. Importantly, high resolution sensing can be accomplished also for the surface plasmon mode, despite its extremely low figure of merit. This is accomplished by monitoring the coupling efficiency of light to plasmons instead of conventional sensing which is based on changes in plasmon energy. We suggest that these nanohole structures can be used for studying molecular transport through nanopores and the behavior of molecules confined in volumes of approximately one attoliter.