There's been a horrific accident! Fred Fredrickson is dead! There isn't even enough left to bury!
Wait, is that Fred over there? What the hell is going on?
Dr. Jonathan "Jon" Osterman aka Dr Manhattan (Watchmen, book and film). He is accidentally locked in a room with a scientific apparatus that removes the "intrinsic field" from matter. It destroys his body, but somehow his consciousness survives and becomes incredibly powerful. He creates a new body for himself.
Sandman (Spider-man 3 film). In a rather suspiciously similar scientific accident, his body is destroyed, but he gains the ability to control sand and makes himself a new body out of sand.
Sauron (Tolkien). In the Silmarillion, the section titled Akallabęth, during the destruction of Númenór, Sauron loses his body and flees as a spirit, bearing the One Ring to Middle Earth. He regains a physical form, but can never again become the ethereally beautiful angelic spirit he once was.
Alphonse Elric (Fullmetal Alchemist, all versions). In an incredibly foolish attempt to bring their dead mother back to life, Alphonse and Edward conduct a forbidden alchemical ritual. Alphonse loses his entire body, and Edward sacrifices his leg to bind Alphonse's soul into a suit of armor.
Johann Kraus of the Hellboy/BPRD universe had his entire physical body destroyed in a mystical accident and has to inhabit a containment suit, otherwise he would dissipate. "He's not dead. He just doesn't have a body anymore."
Excludes characters who purposefully transcend their physical form to become something else, mind-swapping, brain transplants, ghosts, etc.
Literally the entire body, from head to toes including brain is gone.
Might or might not include characters like Arnold Rimmer in Red Dwarf, who died and got resurrected as a hologram. The problem I have with including computerization is that in some fictional universes it can be a routine operation, which would tend to clutter up the page. I suppose simply naming the universe and giving one or two examples would suffice.
Might or might not include characters like the Tin Woodsman in The Wizard of Oz who lost his entire body in a series of accidents.