Using the etch factor feature causes the cross-section of traces to be modeled as trapezoidal instead of rectangular. This can trigger warnings if something about the geometry complicates the process of adjusting the cross section. If you double click on the warning messages the view will zoom to what HFSS believes is the problematic geometry. In the case of the TOP layer HFSS might zoom to a thin sliver of metal. Kindly delete this sliver and try again.
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