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How can I create selection sets based on profiles? (a series of selection sets containing the elements within each profile)
As of January 2019, this is being considered for a future product release - reference Enhancement # 179545.
In the meantime, if the profiles were created using the Auto Create Profiles feature described here (one for each branch of the system), then you could potentially use the Branch Labeling feature (Tools > Tools > More > Branch Labeling) to label the branches, then use a series of queries to select the elements of a branch, right click in the drawing > Create selection set. If your goal is to export the data, could then export your element flextables to Shapefile or CSV format.
If you are looking to create selection sets in order to manipulate a flextable and present the hydraulic data associated with each profile, consider using the Profile Annotation Table, which is customizable in Engineering Profiles, as seen in this article: Ability to customize profile annotation tables