This invention provides a new design and fabrication for a three-dimensional crossbar architecture embedding a sub-micron or nanometer sized hole (called a molehole) in each cross-region. Each molehole is an electrochemical cell consisting of two or more sectional surfaces separated by a non-conductor (e.g. a dialectric layer and solid electrolyte). When used in electrochemical molecular memory device (EMMD), the architecture provides unique features such as a nano-scale electroactive surface, no interaction between memory elements, and easier miniaturization and integration.