How do I remove deactivated users from Department?

[Laura Bowers]

I am currently setting up Atlas and noticed that some teams and departments are showing users who are no longer with the company and have had their access revoked. 

How can I remove the user from the department or from drop downs so we can only access valid, active employees?

[Mikael Sandberg]

Are you using an IDP to sync your users with you Atlassian instance? If you look in admin.atlassian.com, do the users show up as deactivated there? If not, then you can deactivate them via the REST API. You would need to get directory ID and then use that to get the user Id ((not the Atlassian Id) in order to use Update user by ID the value active to false.