I was sort of able to take a cross section of 1 3D image by using
intersection() but it lost the top and bottom of the image.  Luckily I was
still able to export it and using Sketchup, I was able to bring back one
side so I could extrude it as I wanted to do anyway.

But the 2nd image I'm having more difficulty with because the scanner
screwed up and introduced some bulge artifacts (makerbot scanner) which I
tried to correct by taking two scans in different orientations and then
making an intersection of the two after correcting for the translation and
rotation.  However, taking a slice from that caused some of the vertical
walls to disappear too.

I'm more than willing to post the 3D scans and my code as this is definitely
a bug and should be addressed at some time.  Just let me know where to put
them.

A

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View this message in context: http://forum.openscad.org/Trying-to-take-a-cross-section-of-a-scanned-3d-image-and-failing-tp11374.html
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Could you post a screenshot? I don’t quite understand how your can “lose” the top and bottom of an image.
Note that OpenSCAD tends to struggle with importing large STL files. Your 3D scanner software (or any 3D scanner software) is likely to do a much better job at this. If OpenSCAD acts up, one common solution is to run through a polygon reduction process on it, e.g. using MeshLab.

-Marius