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Most proposed realizations of a high temperature superconductor (HTS) qubit require the use of very small Josephson junctions. The properties of bicrystal junctions are especially interesting since they make it possible to implement several types of flux qubits in a relatively simple way. We have developed a technique that allows us to produce high quality sub-micrometer junctions in a reproducible way using bicrystal technology. We have successfully fabricated and characterized a large number of YBCO junctions and SQUIDs with bridge width as small as 0.2 micrometer on 0°-3°, 0°-40° and 0°-45° bicrystal STO substrates. The properties of these junctions have been extensively examined at temperatures down to 20 mK. The effects of external magnetic fields on these structures have been investigated. Figures of merit for the proposed qubits were also extracted from these measurements.