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How do I properly use the "Non-functional Pads" check properly on my Gerber files?

Thanks for your question.  

In order for DFM Checks to properly function you must perform Netlist Extraction beforehand (especially on Gerber files - because other formats like ODB++, 2581 already have the nets included).

To preform netlist extraction. go to menu:  Tools | Nets | Netlist Extraction... 
or during DFM Check, check the option "Overwrite Nets"

Why?  Gerber data is just a bunch of simple geometry objects (i.e lines, aperture shapes, and polygons).  A netlist is an internal map of the connectivity for all objects on metal layers. 

Now when you perform DFM Checks (with Nets), all checks will preform as intended - even on Negative Plane layers.

Thanks again, and let me know if that helps.

Best regards,

Simon

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