All systems are managed?
No they are not managed, but they are appearing on the system tree. how do i go about removing them?
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If those machines are deleted from your AD too, run the Active Directory synchorization task in epo once again.
To delete Duplicate machines select the machines under system tree >Action>Directory Management>Delete.
If you need to find out all duplication then Run Query
Queries and Reports>System Management>Duplicate System Names>
Once you get the list delet them.