It's generally used as an exclamation which will generally only get a yes or no answer unless you quantify it with, when, how at what time etc:
She used to come here? When? or How? or At what time?
Or if you're asking a specific question and expecting an answer to it, I'd use:
When did she come here?
She came here three years ago.
How did she come here?
She came by bus.
Used to is referring to something that happened in the past, which may or may not still happen. So you have to quantify what answer you're expecting in asking the question.
If you simply use:
She used to come here?
About the only answer you'll get is yes or no.
However, you'd probably be better off completely rephrasing the question to be more specific:
Has she been here before?
Three years ago.