A nanowell device for the electrical characterization of metal-molecule-metal junctions was built using readily available processing tools and techniques. This device consisted of a nanoscale well, with a gold bottom, filled with a self-assembling monolayer of organic molecules, and capped with titanium and gold. Focused ion beam technology was used to fabricate the well with a width less than the grain size of gold. This nanowell improved the device performance dramatically by reducing the chances of pinhole formation in the self-assembling monolayer on the bottom gold electrode. Unlike some established characterization techniques, including conducting probe atomic force microscopy and scanning tunneling microscopy, the nanowell device has the potential for future circuit integration. The effectiveness of the device was confirmed by testing I-V characteristics of alkanethiols and oligomeric arylthiols. The alkanethiol current was exponentially dependent on chain length with a decay factor (beta) that ranged from 0.7 to 0.75/angstrom with the applied voltages of 0.1-1.0 V. Additionally, we gained new insight into the electrical behavior of an oligo(phenylene-ethynylene) molecule with a nitro side group. In this work, we present the complete I-V characteristics observed from the nitro molecule showing electrical switching with memory. Unlike previous reports, we did not observe any reversible negative differential resistance. However, the observed switching with memory behavior may have potential applications in logic and memory devices. (c) 2005 American Vacuum Society.