Patient-specific instruments for preparing bones for receipt of orthopedic prostheses, such as the distal tibia and the talus in a total ankle arthroplasty (TAA) procedure. A tibial guide and a talar guide are manufactured based on patient-specific anatomical data obtained using imaging technology, and each guide includes a surface conforming to selected anatomical surfaces or regions of the tibia or talus, respectively. Each guide includes at least one cut referencing surface, such as a cut slot, to guide a resection, and may also include a guide aperture sized to guide a reaming tool for reaming the distal tibia or talus. The guides may also include pin holes positioned within a periphery defined by the cut referencing surfaces such that, when the resections are made and the resected tibial bone portion or talus bone portion is removed, the guide and its associated pins are removed along with the resected bone portion.
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