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This paper proposes methodologies and techniques for multi-block navigation of an indoor localization system with active beacon sensors. As service robots and ubiquitous technology have evolved, there is an increasing need for autonomous indoor navigation of mobile robots. In a large number of indoor localization schemes, the absolute position estimation method, relying on navigation beacons or landmarks, has been widely used due to its low cost and high accuracy. However, few of these schemes have managed to expand the applications for use in complicated workspaces involving many rooms or blocks that cover a wide region, such as airports and stations. Since the precise and safe navigation of mobile robots in complicated workspaces is vital for the ubiquitous technology, it is necessary to develop a multi-block navigation scheme. This new design of an indoor localization system includes ultrasonic attenuation compensation, dilution of both the precision analysis and fault detection, and an isolation algorithm using redundant measurements. These ideas are implemented on actual mobile robot platforms and beacon sensors, and experimental results are presented to test and demonstrate the new methods.