I'm having trouble with Gerber files that are composed of many individual lines instead of fill/polygon polygons. Is there an option in FAB that recognizes and automatically converts these fields to polygons?

FAB 3000 has an excellent tool for these situations to reduce file sizes and cleanup the data, called: Smart Merge (in the Tools menu)

Here's a quick video tutorial (no sound), showing me select  a couple layers (with individual lines) and clean up to polygons:

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