Anyone have any good ideas on how to align the work after flipping it over? The Triforce I cut (http://fozztexx.com/CNC/IMG_3101.JPG) required me to flip it so I could recess the outer ring. Of course I didn't get it lined up quite right. I'm certain at some point I'm going to want to do double sided PCBs and it's going to be important that it aligns perfectly.
What I did was I had it drill a hole on the right side all the way through so that I when I flipped it over the hole would be in a fixed position from the left side. Then I moved the tool out to that fixed location and lowered it and moved the work over to set the hole in the right place. But since the hole was drilled wobbly it didn't line up quite right. There must be a better way where I don't have to worry about holes being perfect.
I would make a hole in each corner, using a drill program to make the holes. Then when you flip the part, if 0,0 was the lower left hole, it could remain the lower left hole in the new orientation. Use pins or dowels to fix the parts to the holes.
At a minimum, I'd drill 2 holes at a set distance along only one axis (say, along X). Then when the part is flipped, all Y-distances are still positive, but all X-distances would be negative.
In either case, the distance from the tooling holes to any feature of your part is known, by design, and the part is rotationally constrained along at least one axis.
If Possible don't machine through your part on the first side, then try machining the side opposite of your X-0 Y-0 then when you flip the part you will know exactly where the part is.