The persistent miniaturization of solid state devices has led us in the direction of integrating soft materials into solid-state structures. Since organic molecules have natural dimensions in the nanometer range or smaller, they can be useful facilitators in the fabrication of nanoscale devices, and due to their versatile functionality they can be incorporated in actual device structures and even serve as active device components. The central theme of this thesis is the integration of soft (organic and biological) molecules with solid state surfaces and devices to create novel hybrid nanostructures. The techniques of self assembly of organic molecules onto solid-state surfaces have been well developed through extensive research in the past. Self assembly and directed self-assembly of organic and biological molecules were used extensively in this work to demonstrate desired selectivity in the assembled molecular patterns and retainment of the bio/chemical functionality of the assembled molecules. A micro-contact printing technique was used to create microscale molecular templates. Selective directed assembly of biological motor proteins was demonstrated, enabling controlled motor motility without creating any physical barrier. The biological motor protein, heavy mero-myosin, assembled onto organic molecular patterns utilizing biotin-streptavidin linkage, was able to support actin motility, demonstrating the successful assembly and functionality of the motor proteins. On the other hand, nanoscale molecular patterns were prepared with dip-pen nanolithography (DPN). The extraordinary precision and high spatial registry of DPN was used to study molecular transport of organic molecules on solid surfaces. We discovered a new phenomenon of nanoscale anomalous diffusion while assembling dodecylamine on mica. Furthermore, DPN was used to functionalize an active region of a micro-Hall device fabricated from an InAs quantum well heterostructure using conventional lithographic techniques. Biologically tagged superparamagnetic beads with streptavidin were assembled onto the molecularly templated Hall cross by using biotin-streptavidin linkage. The beads assembled onto the active Hall cross region were successfully detected using ac phase-sensitive Hall magnetometry at room temperature. This is one of the earliest complete demonstrations of magnetic detection of a specific biomolecular binding. The versatility of the biotin-streptavidin linkage makes this assembly and detection process highly adaptable for the magnetically labeled detection of a wide variety of other biological systems.