If a creature with wither deals damage, do -1/-1 counters remain even if the creature leaves?

Wither is a static ability that changes how a source deals damage. Instead of marking damage (which is removed at end of turn during the cleanup step), wither causes the source to deal damage to creatures in the form of -1/-1 counters. This is governed by CR 702.90 (wither) and the general rules on counters (CR 122).

Once those -1/-1 counters are placed on the damaged creature, they exist independently as objects on that creature. The creature that dealt the damage — or any other game object — has no connection to or ownership of those counters. Even if the attacker is immediately destroyed, exiled, bounced, or phased out after dealing damage, the counters stay exactly where they were placed.

Counters are only removed from a permanent if a specific game effect (a spell, ability, or rule) explicitly removes them. The cleanup step removes damage marked on creatures (CR 514.2), but -1/-1 counters are NOT damage markers — they were placed instead of damage, so the cleanup step does not touch them.

Example: Your 2/2 creature with wither attacks and deals 1 combat damage to your opponent's 3/3. Before the damage is even placed, your opponent uses an instant to destroy your wither creature. It doesn't matter — the 3/3 still receives one -1/-1 counter and becomes a 2/2 for the rest of the game (or until the counter is removed by another effect).

The only ways to remove those counters afterward are effects that specifically say they remove -1/-1 counters (e.g., Vampire's Bite, Fate Transfer) or effects that remove all counters from a permanent. The source leaving the battlefield is irrelevant (CR 122.1, 702.90a).