The only mention of marking--and the scripture which the WTS uses to back up the procedure--is 2 Thess 3:14-15:
But if anyone is not obedient to our word through this letter, keep this one marked, stop associating with him, that he may become ashamed. And yet do not be considering him as an enemy, but continue admonishing him as a brother.
So there's no clear indication of whether the "marking" was an individual or congregational action.
Interestingly, however, the Greek word that the NWT translates as "stop associating with" is the same one that they render as "quit mixing in company with" in 1 Cor 5:11, which is the scripture they use to justify the disfellowshipping arrangement. So it seems rather tortured to attempt to distinguish the two.