I have FileA in branchA and FileB in branchB.
The problem is that I can access only one file at time. I would like to be able to compare the files by FileMerge or mel
You can use "git mergetool" for merging, and in modern git (meaning version 1.6.3 and later) "git difftool" for comparing using graphical tools. Of course you would have to configure them first, but they do some autodetection (with some hardcoded preference, of course), and if I remember correctly opendiff support is built in.
And then of course you would be able to use your graphical tool (opendiff / FileMerge) as you would use ordinary "git diff", for example
prompt> git difftool somebranch:UNREADME otherbranch:README