We have a sharepoint where we have to use 3 AD domains (eg: domA, domB, domC) to pull users from. Sometimes there are users who would appear in all these domains(domA\User1, domB\User1, domC\User1). How can we configure Employee Directory to avoid these duplicate values. Currently, people search employee directory shows three different entries for the same user: "User1" instead I would like to see only one entry per user. Please suggest.
You would have to work with the AD teams that manage those. You would have to identify the duplicate users and move them to specific OU. Then you can configure People Picker to exclude those OUs from the query.