Any other variants to matter vanished?
The matter can be made to vanish by:
Sent away via time travel.
Teleportation beams. I recall that happening in a Marvel comic once; a character was
assumed to be disintegrating people, but he was actually transporting them elsewhere.
Collapsed into an infinitely thin disc (seen in
One Face, when a damaged FTL drive set the local speed of light to zero).
"Rotating an object about its axis", as in
Have Spacesuit Will Travel. The object (a planet in that case) is rotated 90 degrees relative to spacetime so it no longer has any connection to the universe.
Crushed into a stable micro black hole
(Borderland of Sol). Of course while the matter vanishes that doesn't mean it can't still eat you...
Shrunk to microscopic size via Pym Particles (Marvel comics).
Smeared across a multitude of alternate possible universes so that its own probability of existence falls below the threshold for it existing in any one of them (seen in
Jack of Eagles).
Transformed into "shadow matter", which doesn't interact with normal matter save via gravity.
"Time-Space Separation" from
War of Omission, which edited cubical zones out of reality and not only made objects and people vanish, but made people forget they'd ever existed in the first place. Interestingly, it was also reversible (assuming you figured out that it had happened in the first place, of course).
In the Well World series the vast majority of matter in the universe is artificially created and maintained by the Well World computer, and can be made to vanish by a number of methods interfering with that. Since the matter was never "real" in the first place it can be deleted much like a more conventionally simulated object.
Super speed induction, as seen in one Star Trek Original Series episode; the targeted person vanishes because they are now moving too fast for you to see anymore.
Mind control. The matter is still
there; you've just been rendered incapable of realizing it.