Southern Nigeria encompasses diverse geological terrains that significantly influence its subsurface characteristics. Understanding the depth and distribution of magnetic sources is essential for advancing geological and hydrocarbon exploration in the region. This study aims to estimate the depth to magnetic sources across selected locations in Southern Nigeria using two-dimensional (2D) spectral analysis of high-resolution aeromagnetic data. Ten aeromagnetic sheets, obtained from the Nigerian Geological Survey Agency, were processed. Residual magnetic maps were generated by removing regional trends using first-order polynomial fitting. The residual anomalies were subjected to spectral analysis through Fourier transformation using Oasis Montaj and MATLAB environments. Results reveal two distinct magnetic layers: shallow magnetic sources at depths between 0.2 and 0.4 km, and deep sources ranging from 1.6 to 6.2 km. These depth estimates were utilized to construct 2D contour and 3D surface models of the magnetic basement topography. The analysis shows five distinct uplifts and depressions within the crystalline basement, with deeper basement regions concentrated in the central and western parts of the study area. These depressions correspond to thick sedimentary piles, indicative of promising zones for hydrocarbon exploration, particularly in Nsukka, Abakaliki, and Abeokuta. In conclusion, spectral depth modeling from high-resolution aeromagnetic data proves effective for delineating basement morphology in southern Nigeria. This study enhances resolution in subsurface geological mapping and identifies new prospective hydrocarbon zones by integrating advanced spectral techniques with 3D visualization, aiding exploration efforts in underexplored sedimentary basins.