Again it is hard to say what is going on with a schematic of your entire power supply, and the part numbers of all the parts (I meant the inductor, the diode and the caps, although the caps just need a capacitance and voltage rating). TI's webench is very handy, but layout and part selection can still make or break a circuit. So, a photo of the board, and a schematic of what you've got - not what you intend to have.
As for filtering, I would first get the switching power supply working, so it can provide adequate current and regulation for your given input voltage range. Then you can play about with the output cap value, or possibly add a post regulator LC filter if needed.