Can't fix self-intersecting problem

[jeffmorris]

When I repair one of the models in S3D, the model is manifold but I can't fix self-intersecting problem. I tried to fix it in STL editors but they don't work. S3D is supposed to highlight the problem but I can't find the highlighted problem.

[S3D-Alex]

I was able to find the errors here but they are admittedly pretty small so probably won't cause any print issues. I included a screenshot below showing where the error is with the cross section view enabled.

[jeffmorris]

How can I fix self-intersecting problems in Blender3D?

[jeffmorris]

I used Autodesk Netfabb to fix the problems and 3D-printed the brake calipers without any problems. There were "holes" where you showed me the problems.

[CavanBaillie]

I have had no luck using the repair tools in simplify3D.
Repetier Host has a fantastic manifold repair tool built in to their software. I repaired my model then exported as an stl then opened it in Simplify 3D and it works perfectly.