Nanoimprint lithography (NIL) is a fast, simple and high throughput technique that allows fabrication of structures with nanometre precision features at low cost. We present an advanced bilayer nanoimprint lithography approach to fabricate four terminal nanojunction devices for use in single molecule electronic studies. In the first part of this work, we demonstrate a NIL lift-off process using a bilayer resist technique that negates problems associated with metal side-wall tearing during lift-off. In addition to precise nanoscale feature replication, we show that it is possible to imprint micron-sized features while still maintaining a bilayer structure enabling an undercut resist structure to be formed. This is accomplished by choosing suitable imprint parameters as well as residual layer etching depth and development time. We then use a feedback controlled electromigration procedure, to produce room-temperature stable nanogap electrodes with sizes below 2 nm. This approach facilitates the integration of molecules in stable, solid-state molecular electronic devices as demonstrated by incorporating benzenethiol as molecular bridges between the electrodes and characterizing its electronics properties through current-voltage measurements. The observation of molecular transport signatures, showing current suppression in the I-V behaviour at low voltage, which is then lifted at high voltage, signifying on- and off-resonant transport through molecular levels as a function of voltage, is confirmed in repeated I-V sweeps. The large conductance, symmetry of the I-V sweep and small value of the voltage minimum in transition voltage spectroscopy indicates the bridging of the two benzenethiol molecules is by π-stacking.