How to fix transparent outer face? I have a 3D model that is essentially a mostly outer cylinder but with some geometries in the inner wall. However, it seems that MakerBot print software is having trouble interpreting places when the outer wall is just a thin face (with no thickness) and makes the model seem transparent there when looking from the inside, even though it looks solid from the outside. I think for this reason, the model is completely filling in the cylinder in those places, which is what I am trying to fix. 

Any suggestions would be appreciated.
You've not offered the source of the model, nor the software from which it was created, but I suspect that you'll find the "invisible" faces have reversed normals. This is a characteristic of modeling software that believes the outside is the inside and vice versa. If you are comfortable with using another program, you can check/confirm those problematic sections.

I'm fond of Meshmixer, a multi-platform 3D modeling and editing program. It will display reversed normals with a bit of zebra striping. One can use the Select tool, highlight those faces and use the Select Edit, reverse normals menu entry to repair the problem.

Some slicers will automatically repair this type of problem. For a different approach, download and import your model into Slic3r, which will indicate that it has corrected xx errors.