A method to model self-affine tiles by simple iterative systems is developed in order to study their topology. The model is functorial in the sense that there is an easily computable map that induces isomorphisms between the natural subdivisions of the attractor of the model and the self-affine tile. It has many beneficial qualities including ease of computation allowing one to determine topological properties of the attractor of the model such as connectedness and whether it is a manifold. The induced map between the attractor of the model and the self-affine tile is a quotient map and can be checked in certain cases to be monotone or cell-like. Deep theorems from geometric topology are applied to characterize and develop algorithms to recognize when a self-affine tile is a topological or generalized manifold in all dimensions. These new tools are used to check that several self-affine tiles in the literature are 3-balls. An example of a wild 3-dimensional self-affine tile is given whose boundary is a topological 2-sphere but which is not itself a 3-ball. The paper describes how any 3-dimensional handlebody can be given the structure of a self-affine 3-manifold. It is conjectured that every self-affine tile which is a manifold is a handlebody.