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It's easy...you'll need a cow and some C-4 with remote detonator. Insert C-4 inside of cow and then wait until they come to mutilate it. You then detonate the cow. Of course there won't be any evidence left.
The best thing I can come up with is an EMP laser, though it is very likely that the UFO would be shielded against such a thing.
I think I'd inundate the atmosphere with aluminium and barium dust and the set up a resonating electromagnetic pulse using HAARP. That restricts their ability to open portals and knocks out their cloaking device. Doesn't damage them but makes life difficult.