The Morro do Leme laterite nickel deposit lies inside the western border of the Parecis Basin (Brazil). This deposit is characterized by high concentrations of lateritic Ni (about 1.8%) and anomalous contents of Pd, Au, Cu, Na, Co, Zn, and Pt in a peridotite and dunite layered intrusion. Besides the existence of geochemical and drilling data, the 3D distribution in the subsurface of this layered intrusion is still unknown. An airborne magnetic survey revealed three east–west elongated magnetic anomalies, characterized by a significant remanent magnetization. The sources of these anomalies were delimitated laterally and had their depths estimated between 90 and 150 m, using techniques that use derivatives. Further, the total magnetization direction was obtained from a distortion analysis of the magnetic anomalies. All these data were united in an initial model for the 3D inversion of the magnetic data. The total and induced magnetization directions were attributed to the inverted model of 0.12 (SI) susceptibility, allowing indirect estimation of the remanence. The model, defined by the depth, the inversion, and the remanence estimates, linked the intrusion to analogue events in the Rondonian-San Ignácio Province. The results indicated that to explore for laterite Ni, the best locations are the southern part of the main anomaly and in the cover above the two smaller anomalies, whereas to explore for Pd, Au, Cu, Na, Co, Zn, and/or Pt, the indicated region is the central portion of the main anomaly.