Multiple Find Nominals data sets from single scan?

For data analysis purposes, I need to discriminate between two alternating surfaces/materials along a single scan path. I would like to scan once in Master mode, then compare that master set of data against the CAD twice, each time referencing a different CAD surface. I know this could be done by scanning the part twice, but I am trying to save time by eliminating extraneous measurement.

The surfaces alternate quite a few times along the scan path, but there is a gap between them, so I am not concerned about misinterpreting data from one surface as the other.

I have attached an example cross section showing the single master scan in red and the individual data sets that I would like to generate in blue and yellow. For some reason, the forum is shrinking the size of the image to be all but invisible. Sorry for that.