Hi,
You can delete the users or group in the security page of the folders which you don't want the users to see via report manager.
Assume one directory of your report server is Home/ReportFolder1/ReportFolder2/....., by default, the ReportFolder2's Item security is inherited from the ReportFolder1 item, and the ReortFolder1's is from Home item. So you can open the ReportFolder1 or Report2 and click its properties tab and go to the Security page to delete the user or group who you don't want to see this folder.
See http://msdn.microsoft.com/en-us/library/ms156034.aspx from more details on how to grant user permission in reporting service.
Hope this help,
thanks,
Jerry