We apply compensated convex transforms to define a multiscale Hausdorff stable method to extract intersections between smooth compact manifolds represented by their characteristic functions or as point clouds embedded in Rn. We prove extraction results on intersections of smooth compact manifolds and for points of high curvature. As a result of the Hausdorff–Lipschitz continuity of our transforms, we show that our method is stable against dense sampling of smooth manifolds with noise. Examples of explicitly calculated prototype models for some simple cases are presented, which are also used in the proofs of our main results. Numerical experiments in two- and three-dimensional space, and applications to geometric objects are also shown.