Rachael said:
The MC's ex-boyfriend is the leader of a world crime organization. He's a little neurotic, and he kidnapped her a) because he's obsessed with her and b) to upset her current fiance. I had him rape her, then repeatedly tell her her fiance wouldn't want her anymore because of it. Mostly he was trying to brainwash her using torture, etc.
Ah, well, this makes a big difference. The leader of a criminal organization is going to behave very differently than an official intelligence agency - a criminal organization isn't going to give two hoots about the techniques used; an intelligence agency is going to be more selective, more subtle in its techniques (depending on the situation, of course).
And of course, the prior relationship will impact things.... Most certainly he'll want to cause her pain, which pretty much any technique will do. If he hopes to get her back, he won't likely use a technique that would disfigure her; if he wants to ensure no one else will ever have her, the exact opposite would be true.
For brainwashing, it's key that the technique he use include a lot more than pain - do some internet / library research on brainwashing. The first step is to take away the victim's identity - sense of self. Don't let him use her name when she can hear it - not even to others when talking about her. He should immediately take away anything which she might use to maintain her identity - clothing, jewelry, etc. - and replace those that need replacing with something generic, uniform-like. In serious cases, a standard haircut is even used (think military - there's a lot of brainwashing techniques used in bootcamp, just not to the same ends / extremes). Using her violin (wasn't it?) doesn't fit with this, though it does fit with increasing her level of stress (you'll have to decide how consistent his techniques will be and toward what end). Sensory deprivation can also be a part of brainwashing.
For techniques which don't involve disfiguring the victim, look into sleep deprivation and torture involving extremely loud music or other noise (both are more effective than one might believe without having done research). When sleep deprivation is used, it is generally in conjunction with forcing the victim to stay in a single, uncomfortable position for long periods of time - sitting on a stool with no back, standing facing a wall with one knee bent awkwardly and the arms folded at forehead level, leaning against the wall (for example). Also consider hooding (which can be used both for torture and for brainwashing (sensory deprivation)). All of these techniques are good when you want to extract information and have the time for them to take effect as they don't risk injuries which would prevent the victim from answering questions, but do mess up the victim's head to the point where they make mistakes. And I agree with what's been said about drowning.
For more physical techniques or for disfiguring techniques, the links provided and/or a google search should give you lots of ideas - use whatever fits the torturer's personality...
FWIW,
Liz