If your sister was baptised as a Catholic she is a Catholic. As a Catholic she must be married according to canonical form. Therefore, to be married in a civil ceremony she would have required dispensation from canonical form.
If after her baptism and before her civil marriage she formally defected from the Catholic Church she would not have been bound by canonical form.
If she had applied for and was granted dispensation from canonical form the civil ceremony will not invalidate her marriage. (This does not mean it may not be invalid on other grounds but that would be for a diocesan tribunal to determine.)
If she had not formally defected from the Catholic Church and she had not been granted dispensation from canonical form then her marriage is invalid, on that ground alone. In this type of case it is relatively straightforward to get an annulment. She would still have to take the case to the competent diocesan tribunal. They would still need to issue a decree of nullity. But, in cases of lack of canonical form the case is usually quite straightforward and quick.
As you say she is separated a diocesan tribunal would probably not take on the case unless she obtained a civil dissolution (i.e. divorce). After a civil dissolution she could take her case to a diocesan tribunal.
According to Church law if she obtained a civil dissolution she would not be free to marry again until she obtained a decree of nullity from a diocesan tribunal.
However, it sounds like your sister has no regard for Catholic teaching or Church law so she is unlikely to be concerned about any of these matters.