God help you, but this is going to be tough. And it will probably get worse before it gets better, but I wish you all the strength and luck in the world.
Please understand, these are my opinions and what I would do:
First, contact a sexual assault victims services provider. Even if all you can find is something listed for women, start there. They may be able to refer you on. I would also look specifically for support groups or services for victims of incest. Again, if for nothing else than referrals, it won't be a wasted effort.
Once you have some emotional support for you and your daughter, they can then guide you on how to proceed legally. Often, they offer legal advocacy services, which means someone to come with you to the District Attorney's office. They will also be able to help prepare you for the questions you will get and what kind of evidence or documentation you will be asked about.
They should also be able to tell you, realistically, how far this will go. They will know if the DA in your area is notorious for demanding all kinds of incontrovertible proof like eye witnesses or confessions, or if they will proceed with 'soft' evidence such as the child's testimony.
I must also add a word of caution here. There is great debate amongst experts on whether or not it is ultimately more damaging to the child to go forward with charges and a trial. Some say that the trauma of reliving the events, facing their molester, particularly if that molester is a parent, and being subject to cross-examination is worth the emotional cost to the child. Counselors are going to spend a lot of time working with your child to help her understand how she is not in any way responsible for any part of this. Going to court, having a 'say' in his prosecution, in some opinions, undermines that effort. Some say the exact opposite.
Others say that the child, having been the ultimate vicitm, completely powerless, is thus given the opportunity to take back power over themselves. Which I tend to agree with, if there is a conviction and significant sentence. The only problem is, if there isn't a conviction, or there is an inconsequential sentence, helping that child to reclaim that power is very difficult.
In my opinion, most of the answers to the above depend first on the child. Only you, with the help of experienced counselors, can make that decision. The other major consideration is the cost benefit analysis...what is the benefit of the most probable outcome, and is it worth the cost of the trauma it will take to get there. Again, the temperment, personailty and strength of the individual child is the biggest factor in that equation.
I wish you luck. These are the hardest decisions a parent can make. It may turn out that you decide, as many others have, that it is simply not worth the pain and trauma your child would have to go through. If that is the case, take solace in the fact that he is already tried and convicted. With that alone, you should be able to get any parental rights he has stripped. Permanently. That, afterall, is the most important thing here...that he can never hurt your child again. And as a registered sex offender, the rest of the world will also have some measure of protection from him.
And if anyone EVER questions your decisions, remember this. YOU didnt do this to this child, nor would you have allowed it had you known. NO, it is not possible to ALWAYS know these things. These things have been going on forever...there have always been sick, twisted b@astards masquerading as human and you are not in any way shape or form responsible. Base your actions from this moment forward on what you believe to be in the best interest of your child and no one, not even the child, will be able to hold you responsible.