Hi R.,
My daughter was diagnosed with molluscum at 2 1/2, she's now 4 and she still has it. I guess she has a mild case as she only has 3-4 spots at a time. We have chosen to just let it run it's course, although the dr. did tell us about a treatment that bubbles the virus out of the skin. It sounds painful and can cause scarring, but it may be an option if your daughter is particually bothered by them as it may help a praticular spot to be gone sooner - it doesn't prevent a new spot from forming somewhere else, though.
The only time this bothers my daughter is when a particular spot is ready to be done. Then it grows in size and is very itchy for a couple of days. Of couse my daughter can't leave them alone, so she usually ends up scratching it right off, then we just cover it with a band-aid and in a few days it is healed over. She did have one last summer that was in a bad spot on the back of her leg. We ended up covering it with a little "dot" shaped water-proof band-aid because it was always rubbing on something and irritated. We have also found out that as time goes by, the skin around these areas will tend to be dry and itchy (the dr. said that was very common), so we use lots of gentle lotion to help sooth her skin - especially in the winter.
Her dr. assured us that this condition is not painful and only mildly irritating when the spot becomes itchy.
Good luck!
Chris B.