I doubt they are legally separated. That process is identical to a divorce.
If they are legally separated then there is no need to file for divorce, one only converts the legal separation to a divorce using FA-4162 or FA4163 dependant on whether it is stipulated or not.
If they are legally separated, then there is already a Judgment of Legal Separation, and that implies an order related to custody/placement. Give that order to the sheriff and go get your kids.
Otherwise please restate your question.
I agree they are unlikely to be legally separated. He needs to file for divorce and ask for a hearing on placement. Are the kids at school or daycare? He can go pick them up.
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IF there is truly a legal separation, then the father should enforce the order regarding custody and placement.
If the divorce papers have been filed, then the father has the ability to seek an order regarding custody and placement in that action. If the mother is not willing to agree to a temporary order, then the father can seek a temporary order from the family court commissioner. In WI, so long as there are no issues of abuse, addiction or other like problems, it is presumed that the parents should be awarded joint legal custody (which refers to the ability to make the major decisions) and the court should maximize placement (time each parent spends with the child/ren) with both parents.
Once an order for placement an order of contempt can be sought if the other parent interferes with that placement. Furthermore, if a parent intentionally and unreasonably interferes with a parent's court ordered placement, the other parent can file a Petition to Enforce the placement, and if those allegations are proven, the court SHALL require the parent that interfered with placement to pay the legal fees and costs for bringing that enforcement action.