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We present a technique for fabricating molecular junctions for molecular electronic devices. Silica microspheres are rendered magnetically susceptible and electrically conductive by the sequential deposition of nickel and gold films. The metallized microspheres undergo directed assembly into lithographically defined magnetic arrays functionalized with self-assembled monolayers of prototypical molecular wire candidates. We characterize the resulting junctions by scanning electron microscopy and measure their current-voltage characteristics. Magnetic directed assembly provides a wafer-level route for the fabrication of molecular junctions and opens up the potential for hybrid complementary metal-oxide semiconductor/molecular electronic applications. [ABSTRACT FROM AUTHOR]