Understanding 2D cross-sections of 3D structures is a crucial skill in many disciplines, from geology to medical imaging. Cross-section inference in the context of 3D structures requires a complex set of spatial/visualization skills including mental rotation, spatial structure understanding, and viewpoint projection. Prior studies show that experts differ from novices in these, and other, skill dimensions. Building on a previously developed model that hierarchically characterizes the specific spatial sub-skills needed for this task, we have developed the first domain-agnostic, computer-based training tool for cross-section understanding of complex 3D structures. We demonstrate, in an evaluation with 60 participants, that this interactive tool is effective for increasing cross-section inference skills for a variety of structures, from simple primitive ones to more complex biological structures.