I will describe a construction of invariants for three-manifolds with (parameterized) boundary. The invariant associates a differential graded algebra to an oriented surface, and a (suitably generalized) module to a three-manifold whose boundary is that surface. This invaraint also enjoys a "pairing theorem" relating it with HF-hat of closed three-manifolds. I will describe the basic properties of these invariants, and also the role of certain bimodules which appear in theory. This is joint work with Robert Lipshitz and Dylan Thurston.