Perhaps among his most recognized results in 3-manifolds concern the classification of incompressible surfaces in certain 3-manifolds and their boundary slopes. Bill Floyd and Hatcher classified all the incompressible surfaces in punctured-torus bundles over the circle. Bill Thurston and Hatcher classified the incompressible surfaces in 2-bridgeknotcomplements. As corollaries, this gave more examples of non-Haken, non-Seifert fibered, irreducible 3-manifolds and extended the techniques and line of investigation started in Thurston's Princeton lecture notes. Hatcher also showed that irreducible, boundary-irreducible 3-manifolds with toral boundary have at most "half" of all possible boundary slopes resulting from essential surfaces. In the case of one torus boundary, one can conclude that the number of slopes given by essential surfaces is finite.
Hatcher has made contributions to the so-called theory of essential laminations in 3-manifolds. He invented the notion of "end-incompressibility" and several of his students, such as Mark Brittenham, Charles Delman, and Rachel Roberts, have made important contributions to the theory.