Do you have mulitple eye diagrams because you are probing multiple points or due to sweeps. If it is muliptle probing points, you can always delete out the report definitions for the ones you don't want. Using the rectangular stacked eye diagram plot type might also be useful here.
If this is due to sweep, you can always use the families tab in the plot definition form to sub-select the variations you want to plot.
If you are looking for something different, please share more details.
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