If someone doesn't have a clear mind about how to do something, is it correct to say that I helped her to "clear her ideas"? Or some better expressions?
When used as a verb, "clear" generally means to remove something, so "clear her ideas" probably wouldn't make a lot of sense (but if it did, it would probably be interpreted to mean "remove her ideas", which is probably not what you meant).
As StoneyB and Tyler have mentioned, if you want to say that you make something clear, the correct verb for that is "clarify":
I helped to clarify her ideas.
Depending on exactly what you mean, however, there might also be better words than "ideas". Usually, saying "clarify her ideas" implies that she had good ideas, but needed help expressing them or making them clear to other people. If, on the other hand, her ideas were not good ones, because she didn't really understand the situation, and once you helped her understand then her ideas became better, then you would probably want to say something like
I helped to clarify her understanding.
instead. Likewise, if she understood the problem, but her ideas weren't right because she just wasn't thinking about the problem the right way, then you might instead say:
I helped to clarify her thinking.
Note, however, that while "clarify her understanding" is usually not something somebody would take offense to, you might need to be careful when saying things like "clarify her thinking", as this can sometimes have negative implications (somebody might assume from that statement that you believe that you can think better or more clearly than she can, and are therefore better than her). If in doubt, you should probably just say "understanding" instead...
There is the English idiom:
clear one's head (or mind)
which one website defines as relax so you can think clearly.
You might come across it in a context like this:
I can't figure out how to solve this problem!
Maybe you should take a short walk around the building. The fresh air might help you clear your head.
We clear our heads so that our brains can think more clearly.
Is it correct to say that I helped her to "clear her ideas"?
That depends on what you did. You may have helped her clear her mind, enabling her to find a solution.