Our son had similar problems from birth. At your daughter's age, we made sure there was no stimulating activities after dinner - rough play, television, movies. Now that he's older that includes video or computer-based games, even stimulating board games. It is just too much brain stimulation.
I reviewed his evening meal for stimulating foods including sugar-based drinks (we took out apple juice, for example). Some kids wake up because they're hungry, so plenty of protein at dinner to last through the night. At that age my son didn't like meat, so I had to search for meals that he would eat, like dinosaur-shaped chicken pieces.
Between dinner and bedtime, we focussed on family togetherness activities, like playing board games, reading books together (nothing scarey) and other toy play. My son is very creative, so we tried to balance mind-stimulating play and comfort activities. We read stories together and prayed at bedtime. This isn't about spoiling the child but about making them feel loved and valued.
At 3, your daughter should be able to articulate some of her thoughts and fears and you can query her upon waking about how she feels and what she's thinking. Our son was highly articulate at that time of night - it was amusing what came out of his mouth! But very insightful.
If she wakes you up, I would make her do something that makes her uncomfortable as part of the process - and I do not mean punishing her. This will help to make her think when she wakes up the next time, does she really want to have to do X? For example, at 3, my son was still waking up to potty. I would sit with him and force him to wake up and talk to me so that when he went back to bed he had to snuggle back to sleep. He didn't really want to wake up, but it made him think twice about the next time he woke me up whether he wanted to really wake up.
Also, I would make sure she is getting enough sleep but waking up at the same time every day, including weekends. If she's getting a nap, you might cut back on naptime in order to force her to sleep more soundly at night.
I don't know if these suggestions will help you, but I certainly empathize. My son woke up at least once per week until kindergarten, even though he had been in daily pre-school. Once school started, it built his self-esteem that he could do more on his own and this need for comfort went away naturally. I think this is also a clue. Smoothering her with love and hugs may make her very dependent on you emotionally, especially at 2AM.