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In this paper, we present a 3-D localization method for a magnetically actuated soft capsule endoscope (MASCE). The proposed localization scheme consists of three steps. First, MASCE is oriented to be coaxially aligned with an external permanent magnet (EPM). Second, MASCE is axially contracted by the enhanced magnetic attraction of the approaching EPM. Third, MASCE recovers its initial shape by the retracting EPM as the magnetic attraction weakens. The combination of the estimated direction in the coaxial alignment step and the estimated distance in the shape deformation (recovery) step provides the position of MASCE in 3-D. It is experimentally shown that the proposed localization method could provide 2.0-3.7 mm of distance error in 3-D. This study also introduces two new applications of the proposed localization method. First, based on the trace of contact points between the MASCE and the surface of the stomach, the 3-D geometrical model of a synthetic stomach was reconstructed. Next, the relative tissue compliance at each local contact point in the stomach was characterized by measuring the local tissue deformation at each point due to the preloading force. Finally, the characterized relative tissue compliance parameter was mapped onto the geometrical model of the stomach toward future use in disease diagnosis.