Under the Trump administration's new "zero tolerance" policy, all parents caught crossing the border illegally are prosecuted on a federal misdemeanor charge — meaning they're sent to jail. Parents are separated from their children at that stage because kids can't be sent to jails.
When they appear in court, parents have the option of pleading guilty to the illegal entry charge, which could hurt their chances of legally entering the country in the future, or pleading not guilty, which would likely prolong the separation between parent and child. Many plead guilty in a process critics call"assembly-line justice," receive a short sentence or "time served" and are sent back to Department of Homeland Security immigration detention centers. From there, they have the option of pursuing asylum claims. If that's not successful, they're likely to be deported as an "expedited removal."
Once kids are separated from their parents, they're classified as "unaccompanied alien children" and sent to U.S. Department of Health and Human Services shelters. That's supposed to happen within 72 hours of apprehension. They're kept in federally run shelters until they are placed with outside sponsors, either relatives who are already in the U.S. or foster parents.