Even if it did work (using an extrusion printer to lay down an etch mask), it seems like it would be about the most expensive and slow mechanism possible for doing it. You would need to operate at the highest level of resolution, which means running it very slowly, and even then I don't think it could compete with other DIY techniques.
For actual milling, a typical 3D printer won't be able to do it. Extrusion printers are designed for rapid print head movement, with minimal mass in the head (and other moving parts). They aren't designed for applying any significant force - certainly not the lateral forces needed to perform CNC milling. If you tried it, you would almost certainly severely damage the extruder carriage assembly.
You could maybe use a 3D printer as a basis for a pick & place system. Pick & Place is similar to extrusion printing in that the carriage speed and accuracy are more important than lateral force. I imagine one of the Delta designs would work really well for it.
Other than that, you really would need a machine designed to do CNC milling as well as 3D printing. I know of only one such machine (perhaps there are some in the > $10,000 range)... the R.P.M. from QU-BD (
http://www.qu-bd.com/). And that one isn't actually shipping yet. The first units are going out to early adopters in a few weeks.