Criminal cases are investigated and prosecuted differently from civil cases. More and stronger evidence is needed to get a criminal conviction than to win a civil suit. If the defendant is acquitted, the Government has no right of appeal.
A federal criminal conviction also requires a unanimous decision by 12 jurors (or by a judge only if the defendant chooses not to have a jury). A judge usually hears civil cases, but occasionally a jury will decide the case.
Both criminal and civil cases can be resolved without a trial where both sides and the judge agree; this is done by a plea agreement in a criminal case and by a consent decree in a civil suit.
In criminal cases, judges must use the Federal Sentencing Guidelines in determining the defendant’s punishment, whereas judges in civil suits may or may not adopt remedies as recommended by the government when it wins.