Once you’ve added a sufficient number of Windows Server 2012 R2 domain controllers to your organization’s Active Directory forest, migrated the FSMO roles, ensured any custom partitions are also hosted on your Server 2012 R2 domain controllers, and made a couple of those 2012 R2 DCs global catalog servers, you can get rid of the existing Server 2003 DCs.
The simplest way to do this is to demote each Server 2003 domain controller back to member server status, remove it from the domain, and then go through whatever decommissioning process your organization goes through with computers.
You demote a Windows Server 2003 domain controller in the same manner that you promote one. As it’s most likely been some time since you promoted a Windows Server 2003 member server to domain controller, and the process has completely changed with Windows Server 2012 R2, the trick is to run dcpromo.exe from a command prompt using an account that is a member of the Domain Admins or Enterprise Admins group.
The demotion process is pretty straightforward, just a matter of working your way through the wizard. Once you’ve retired all your 2003 domain controllers, you can start thinking about bumping up the functional level - a topic – I'll cover in the next blog post.
You can find out more about demoting a Server 2003 DC by reviewing the following TechNet document: http://technet.microsoft.com/en-us/library/cc740017%28v=ws.10%29.aspx