Anybody ever successfully break a cat's bad habits?

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My cat has a little... *problem* with thinking outside the box, as it were. Now, she goes Number Two in her litterbox, and sometimes she pees there too, but a lot of the time when I go clean her box, there's no pee in it. She has peed on the carpet in the past, especially when she began going into heat (she is spayed now), and I think she just made a habit of it and never quit. I had to start putting her in the other bedroom and shutting her in at night fairly early on because I didn't trust her to have the run of the apartment. Now that bedroom carpet's a mess. I have a plan for reclaiming the carpet and maybe breaking her of this (nicely, of course--last thing we need is a neurotic cat trying to break a habit), but I guess it would be nice if someone out there's ever been in the same boat as me and had to deal with this and was successful at it. Because I'm not looking forward to going through with all this crap only to find she still pees on the carpet at the end of it. Sigh.