This is a 2 sided 2"x 3"  PCB with small surface mount parts
Click pics for FULL size
This is the EAGLE file I was using. Single  axis board
Drilled from the TOP, routed on the BOTTOM
EAGLE is showing there is not enough clearance for the .02" bit. You can see on the finished board where it did not route.
You can set the DRU Design Rule Check
See the TOUR on the EAGLE site, Checking the board
I like to use Basic CNC Viewer to check the drill & routing code
http://www.cncedit.com/BasicViewer/Default.aspx
Board right after drilling. Wide shot
Board right after drilling. Close up
Bottom side of board after routing
Bottom of board close up
Board after route. Note 1/2 board has burrs, right side
I used a razor on the left side to show the difference
I though about doing video, but it's usually low quality on the web & doesn't really show anything.

Note: This machine was all "off the shelf parts".
I pulled parts like I would for any other machine being shipped.
Nothing special.
Machine assembly & setup took about 1/2 day.

I added a thick 1" piece of HDPE on the table
and a 3/8" thick HDPE "pin table" on top of that.

I get my router bits from http://carbideworld.com/
I used a 45° bit for this board. I think I like a 90° bit better, less burrs
I drilled through the top & routed the bottom side.
I only have 2 sided PCB stock, so on a board that is single sided I just drill a bigger hole .02" deep on every hole on the top side to isolate the pins.
I didn't do that on this board as it just shows that it will do a 2 sided board with no problem.

I router the traces at 14 IPM. The machine is capable of 18 IPM with a 24V motor power supply,
but the thin 45° single flute bit was creating too many burrs.
Counter start May 4, 09
I am building a NEW CNC site at

http://bluumaxcnc.homestead.com/BluumaxCNC.html

With much more setup detail

It is currently under construction, but most of the setup instructions are done