Two (2) aeromanetic maps on a scale of 1:100,000 covering parts of the Lower Benue Trough (Afikpo sheet 313 and Ugep sheet314) were digitized manually along a total of 70 profiles lines to obtain 5422 data points. The digitized values were contoured to obtain the total magnetic field intensity map of the study area.The merged data was processed and filtered using diferent softwares to perform anomaly separation techniques to obtain the residual fields,petters half width and maximum slope methods were analysed to obtain depths to basements, also lineaments trend and 3-D surface plots were analsed. The results indicate a dominant NE-SW orientation, four faults were also identified mostly at the edges of sediments-basement contacts. The depth to magnetic basement map reveals two identified sub-basins within two structural highs. The Afikpo area has a structural high (afikpo anticlinorium) with depth ranging from 0.8km -1.8km which is flanked by a depression (graben) 2.0km -4.0km, this sub-basin extends between Abanwan to Amagu (ebonyi state) and extents to Biakpan (cross river state).also another structural high occurs between Iyamoyong and Okumeritit (cross river state) 0.8km -1.8km as horst, this is flanked by another depression (graben) within the Mkpani -Ugep area (cross river state) 2.0km -3.0 km in sediments thickness. Hydrocarbon prospectivity within the study area should be within the identified Grabens that has shown greater sediments accumulation while the areas identified as horst has less potentials for hydrocarbon prospectively.