No prescription other than Congress having the power to declare war. We wouldn’t want Congress to do that, now, would we...?
Somebody slap me here, I'm defending a position of Ron Paul's, but he did in fact call for Letters of Marque and Reprisal in the matter, which is to my reading the closest Constitutional allowance for the situation. There are difficulties with those under international law as well, but that too is a matter for lawyers and I won't offer an opinion.
Muawiyah has pointed out that although the function of a declaration of war is provided for in Article I its form is not stated, and if I understand muawiyah's argument correctly, that in the case of Iraq Congress did provide approval that qualified for that under the Iraq Liberation Act of 1998. That also may be a matter for lawyers, but it was, in fact, explicit authorization of military activity against a foreign state, so it has to be at least close.
In the case of al Qaeda, however, it's a lot more complicated. In the case of American citizens in al Qaeda, it may be that a treason trial is appropriate. What, however, constitutes due process for foreign citizens in the matter of Letters of Marque and Reprisal? I will have to admit I don't know and will have to research the matter.