<p>We study unknottedness for free boundary minimal surfaces in a three-dimensional Riemannian manifold with nonnegative Ricci curvature and strictly convex boundary, and for self-shrinkers in the three-dimensional Euclidean space. For doing so, we introduce the concepts of boundary graph for free boundary minimal surfaces and of graph at infinity for self-shrinkers. We prove that these surfaces are unknotted in the sense that any two such surfaces with isomorphic boundary graph or graph at infinity are smoothly isotopic.</p>