While sitting on your bike for hours at a time is never particularly pleasant on the bottom side, mountain biking doesn't need test your ability to endure pain.
It is important to note that male or female, your body does need some time to adjust to riding a bike. If you haven't ridden a bike for some time it may take two or three rides within a couple weeks for your body to adjust to sitting on a bike seat. However, once this adjustment period is over, a little soreness from sitting on the seat for a long ride may be normal but you shouldn't have any significant pain during or after a ride.
There are two issues that should be dealt with in any women's specific mountain bike seat. First, there should be room for extra stuff along the top of the seat. Second, the seat needs to be wide enough to properly come in contact with a woman's wider hip structure.
The first issue is usually dealt with by creating a relief or depression down the center of the seat. This works well. A good number of non-women's specific seats also have this feature since men have some numbing and fertility issues related to the same area.
The second issue is sometimes overlooked and can be the greater source of pain. If a seat is too narrow it can wedge itself between the bones that your body is supposed to rest on in the saddle. This will create some serious pressure points and can quickly lead to unbearable pain. If you are a woman with a more narrow hip structure you may find that you don't need a particularly wide or women's specific seat.
To find a seat that will fit you properly try to find one that is mounted on a bike that you can sit on. If you find a seat you think might be a good fit but isn't mounted on a bike, ask someone at the shop to set it up on a bike for you. Then, sit on the seat and make sure it feels right. Pay close attention to where the bones in your lower pelvic area contact the seat. They should contact a well padded section on the top of the seat and shouldn't be too close to the edge or on the side.
This is an important issue for women since it can make the difference between a ride that is enjoyable or literally a pain in the ass.