I want to disable "Setup" Link from the user Menu.I have unchecked "View Setup and Configuration" permission from System Permissions for the profile of that particular user but Setup link is still there. Any suggestions?
From the HELP DOCS
It is possible to hide the "Setup" link from end-users with the Improved Setup User Interface. Previously, users with minimal permissions would still need access to "Setup" in order to access their personal information. If we enable the Improved Setup User Interface, personal information will now be available under My Settings, eliminating the need to access Setup
In order to hide the "Setup" link, ensure that both are true:
Enable the Improved Setup User Interface:
Disable "View Setup and Configuration" from the users' profile(s):
Also check permission sets (from your answer/comment)