What you're asking slic3r to do is effectively to slice up a solid body, but instructing it not to fill the inside. This works in a lot of cases, and is the preferred method as it's quick and easy.
However, if you want more control over the open faces as you describe, it may not be possible to use this method.
I'd suggest your next step should be to model the shell explicitly in the design software, and then slice that (it should see these thin walls and place a single perimeter in them). In CAD, I'd create a solid body and use a 'shell' tool, instructing it to exclude the desired open faces. If you're using a surface modeller I'm not so sure - you might have a bit of a job creating offset surfaces and patching the ends.
I had a quick stab using solidworks, and although it took slic3r a while to work it out, it did produce something I think would print similarly to yours (see attached).
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SD3. Mk2b + glass, heated enclosure, GT2 belts, direct drive y shaft, linear bearings, bowden-feed E3D v5 w/ 0.9° stepper
Smoothieboard via Octoprint on RPi
