FAB 3000 was originally built and optimized for Gerber files. However if you notice FAB 3000 slowing down drastically during Gerber import and/or more importantly DFM Checks, etc. -- would indicate the plane layers consist of extremely complex polygons with connected holes - sometimes a simple plane layer can have a single polygon with vertex counts of over 500k. According to the Gerber format specifications these type of complex polygons with connected holes are "deprecated" and should not be used (see below).
Fortunately FAB 3000 has an option to "Optimize Polygons (remove cutlines)" during Gerber import which will allow FAB 3000 to eliminate the cut-lines and optimize the polygon. Check this option during Gerber import (see below), and after import - DFM Checks and other commands will run up to 100X faster.