High resolution airborne magnetic data of some regions of Southeast Nigeria were analyzed to map structures controlling mineralization. Such data can be used for mineral assessment programs, surficial geologic boundaries, hydrocarbon exploration at reconnaissance stage, mapping of hydrothermally altered rock zones and geologic structures. First and second vertical derivatives, upward continuation, source edge detection, analytical signal, Centre for Exploration Targeting (CET) and standard Euler deconvolution operations were done to delineate the spatial distributions and depths to the different magnetic sources. The enhanced maps showed major and minor magnetic anomaly centres in the Lower Benue Trough (LBT) and Ikom-Mamfe Rift (IMR) characterized by thin (151–745 m) sedimentation. Also, within these areas there exist some isolated pockets of intermediate depths (745–1634 m) occurring in the neighborhood of these magnetic anomalies. The Calabar Flank (CF) characterized by minor remnants of post-Cretaceous intrusions has sedimentation of over 6126 m in some locations. The 2000 m upward continued TMI map revealed the existence of major deep-seated weak zones believed to have originated during the rifting episode connected with the formation of the Benue Trough. The abundance of intrusive bodies in the LBT and IMR render these parts of the study area unattractive for hydrocarbon exploration. Nevertheless, they possess high base metal mineralization potential while CF is a favorable site for hydrocarbon search.