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This paper addresses the problem of over-the-horizon radar (OTHR) target position registration in the presence of ill-defined ionospheric structures. At present, OTHR is subject to frequent position uncertainties due to ionospheric abnormalities, such as tilts and ambiguous multipath propagation modes, that are difficult to model adequately during radar operation. The detection and registration of discrete terrain features in parallel with routine radar operations were studied with the goal of significantly reducing radar target position errors under most circumstances. The Wide Aperture Research Facility (WARF) experimental OTH radar testbed was modified to enable the automatic detection, processing, display, and registration of terrain features and HF repeater (beacon) echoes in parallel with aircraft detection and tracking operations. Many distinct terrain feature locations were studied in significant detail, including cities, mountain peaks, and an island, and the automatically determined position correction offsets were statistically compared with collocated beacons that served as ground truth. It was found that 100% of the offsets had expected errors of less than 5.7 nautical miles (1 nautical mile equals 1.852 km); and 93% of the offsets (with better ionospheric propagation) had expected errors of less than 3.2 nautical miles. We conclude from the research that terrain features can be used to provide coordinate registration benchmarks over an OTHR coverage area in the same way that beacons can be used.