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In this paper we describe the use of a 3D integral equation forward modeling technique to analyze negative apparent conductivity anomalies and their causative structures. We consider EM measurements as weighted averages of the subsurface electrical conductivity distribution and that each type of measurement corresponds to a different 3D weighting function. The robustness of our method is evaluated using negative apparent conductivity data acquired with a Geonics-EM34 meter at Sugisawa across a Dacite dike intrusion. The patterns of modeled true electrical conductivity as achieved from the 3D forward modeling method are shown to compare favorably with the available geological information and existing knowledge at each area.