MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
I assume (forgive me if I'm wrong) that you are printing this in PLA and quick/coarse settings/profile (layer height >= 0.30mm). I don't remember how thick I designed the top layers that should hold the "tiles" but you should get at least 2 solid layers. The extruder temperature should also be high enough to ensure that that each layer bonds well with the previous one and low enough to be able to remove the raft easily. Btw, I never use a raft. I printed mine in ABS on kapton, blue painter's tape should do the trick for PLA. Talking about materials, tolerances (for ABS) are quite small and PLA may not be flexible enough and break when inserting the iPod into this thing. I hope you can get around the issues you're finding with this and we see another "made" popping up in the makes section. Good luck and thank you for giving this thing a try!