3D image on top/overlapping of 2D Base w/text

[crazyred]

I am trying to duplicate this project I found on the DesignandMake website. I have all the components needed but I simply cannot figure how to assemble then do the tool paths. I believe my problem is that the "base" of Harley-Davidson is not 3D, but I am completely dumbfounded at this point.

[Frunple]

Check out the "base height" setting for the components. Play with that and watch what it does.
Also the combine mode.