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This article discusses the software architecture of an autonomous robotic system designed to explore and map abandoned mines. A new set of software tools is presented, enabling robots to acquire maps of unprecedented size and accuracy. On 30 May 2003, the robot "Groundhog" successfully explored and mapped a main corridor of the abandoned Mathies mine near Courtney, Pennsylvania. This article also discusses some of the challenges that arise in the subterranean environments and some the difficulties of building truly autonomous robots.