I have a 6 layer design where I want to check nets crossing plane gaps. But, I only want to check against certain layers. Specifically layer 1 and 2 where layer 1 is signal layer and layer 2 is split PWR/GND plane. But all I see is to check against the total design.
The answer I provided in the below response should be very helpful here. You will want to create Object Lists for the nets on layer 1 and layer 2 of your design, then run the Nets Crossing Gaps rule on that Object list(s). By default, the rule will run on the whole design which is not applicable to your case.
This video will show you how and why:
Getting Started: Organizing and Using Rules - HyperLynx DRC - Mentor Graphics
Previous answer that is useful:
How do I prevent differential pairs from being checked for single-ended impedance in Hyperlynx DRC