This is a specifically French construction: http://french.about.com/library/weekly/aa032500.htm
Most of the time means it's, but in this sentence it would mean she because it mentions that it's a girl and in english you wouldn't say "it is a girl"
Unless it's a baby or an animal, or where it was unclear until just this moment what they were.
The following is the information provided by Duolingo [under 'Explain' when one clicks on 'C'est' in this sentence]:
C'est instead of il/elle est C'est is used when the noun has an article (le, la, l', un or une) or a possessive before it. Say: C'est ma femme, not: Elle est ma femme.
c'est = this/that/it is
c'est + modified noun = he/she/it is
there is/there are = il y a
Disregard the gender of the speaker's voice (in the situation where a female voice says "je suis un garçon"). The voice is only reading a sentence for you to translate. It is not a case of gender confusion.
so does it means that "elle est une fille" and "c'est une fille"' is the same?
No, it means that c'est une fille is the only correct way to express this idea. It is all according to French linguistic rules.
Here are two links on this matter, the first in French, the second in English: http://www.academie-francaise.fr/il-est-cest-un-0 and http://www.frenchtoday.com/blog/cest-versus-il-elle-est