The Amphitheater Mountains and southern central Alaska Range expose a thick sequence of Triassic Nikolai basalts that is underlain by several mafic‐ultramafic complexes, the largest and best exposed being the Fish Lake and Tangle (FL‐T) mafic‐ultramafic sills that flank the Amphitheater Mountains synform. Three‐dimensional (3‐D) modeling of gravity and magnetic data reveals details of the structure of the Amphitheater Mountains, such as the orientation and thickness of Nikolai basalts, and the geometry of the FL‐T intrusions. The 3‐D model (50 × 70 km) includes the full geographic extent of the FL‐T complexes and consists of 11 layers. Layer surfaces and properties (density and magnetic susceptibility) were modified by forward and inverse methods to reduce differences between the observed and calculated gravity and magnetic grids. The model suggests that the outcropping FL‐T sills are apparently connected and traceable at depth and reveals variations in thickness, shape, and orientation of the ultramafic bodies that may identify paths of magma flow. The model shows that a significant volume (2000 km³) of ultramafic material occurs in the subsurface, gradually thickening and plunging westward to depths exceeding 4 km. This deep ultramafic material is interpreted as the top of a keel or root system that supplied magma to the Nikolai lavas and controlled emplacement of related magmatic intrusions. The presence of this deep, keel‐like structure, and asymmetry of the synform, supports a sag basin model for development of the Amphitheater Mountains structure and reveals that the feeders to the Nikolai are much more extensive than previously known.