Tensorflow: How to give variables scope

I have to first pretrain a network before training it. I do this using code in separate files with their own sessions, but the variables from the first session are still getting carried over and causing problems (as I'm running both these files within one 'main' file).

I could get around this problem by simply running my pretrain file which saves the trained layers and then running my training file which loads the saved layers in. But it would be nice to be able to do these two things in one step. How can I 'break the link' and avoid unwanted variables having a global scope?