This depends on the kind of variables you want to freeze. I you can define this variable with the types of internal coordinates known by TM (see the section about internal coordinates in the documentation), then it is possible. (Note that you can also define coordinates as linear combination of the 'generic' coodinate types known by TM.)
But if you want to freeze cartesian coordinates, you have to run the whole calculation in cartesian coordinates and you can only fix a whole nuclei, i.e. x, y and z, not individual coordinates.
Christof