Dynamics AX 2009 Enterprise Portal was designed with templates compatible with SharePoint 2007, and they are in this compatible mode in SharePoint 2010. Hence not all features are compatible for example with SharePoint Designer. Hence you are unable to edit the master page using this tool. Even if you could edit the master page using the SharePoint Designer, every time you update Enterprise Portal, say using AXUPDATEPORTAL.EXE, it would override the default master page with the copy stored in the AOT.
So therefore to edit the master page do the following:
1. Go to: AOT\Web\Web Files\StaticsFiles\defaultax2. Export defaultax object3. Make a backup copy 4. Edit this defaultax object, which is the master page, in NotePad for example5. Import the new modified master page back into the AOT6. Run AXUPDATEPORTAL.EXE to deploy the edited master page