Thanks for your answer,
So these drawn Pads are responsible for the large files.
I looked in the gerber generator of my PCB lay-out tool (Mentor Pads) and found a way to produce polylines instead of raster filled areas
This result in much smaller output files.
Thanks for contacting me and sending sample files.
The Cyan Layer (overlapping topmask.gbr) is the larger file. If you notice all pads are "line filled" which is extremely inefficient and results in huge files.
Using FAB 3000 you can convert those drawn pads to flashes and that would reduce file size by 100X.
However more importantly would be to determine how there files were generated with line files and eliminate it at the source - so that you would not need to repeat unnecessarily having to convert drawn pads to flashes.