Windows 10 Enterprise E3/E5 comes with free upgrade benefits for users to upgrade from Windows 7/8 Pro to Windows 10 Pro.
To upgrade from Windows 7/8 Pro to Windows 10, the user/admin can do the following:
1. Go to O365 admin center @ portal.office.com as an admin
2. Click on “Windows 10 Upgrade” under admin home
You will be redirected to https://www.microsoft.com/en-us/software-download/windows10 for your user to upgrade to Windows 10 or you to use tool to create Windows 10 installation media.
Since Windows 10 Enterprise E3 is an upgrade from Windows 10 Pro, what you essentially need to do is to download and install the ISO for Windows 10.
More details about the free upgrade benefits can be found here