I can access the users in the domain by typing the contact name in the search box.
Is there a way in the Lync account to organize the users in the same domain into groups as Organizational Units?
Example:
Sales Department:
-User 1
-User 2
-User 3
HR Department:
-User 1
-User 2
Finance Department:
-User 1
-User 2
-User 3
-User 4
If you are talking about the Lync Client, then no (and you are asking in the wrong place). If you are talking about the Lync Client SDK, it's a no but you can workaround it.
What I have done before is to do a LDAP query using DirectorySearcher to generate a list of email address, then using GetContactByUri to generate a list of Lync Contacts to display in our own GUI. This does assume email address matches the Lync sip address, which it may not.
