I believe that Danforth intimidates Mary Warren by using harsh and accusing words towards her at the start of Act III, Scene 3. He tries to threaten her and he tries to make her feel guilty.
He starts to intimidate her by making her feel guilty for what she has done. He implies that (if she was really lying before) that she has condemned innocent people to be hanged. He does not believe this, I think -- he is just trying to badger her.
Later on, he starts to threaten her. He tells her that if she had been lying she will be sent to jail herself for perjury. This is clearly intimidating because he seems to be telling her that she had better not change her testimony or else she'll be in big trouble.