You can set up checkpoints as per Federal law (though your state may vary--some states have provisions against it, in which case your recourse is to state, not Federal law). However, these checkpoints must be indiscriminate: they have to stop everybody that passes them while they're active.
A cop cannot just pull a single car over to see what's going on. He has to have reason.
The stop in question here was clearly unconstitutional, as the appellate court held in their decision for the defendant. Other non-DUI style checkpoint stops without reasonable suspicion of a crime would similarly be unconstitutional.