Does wither damage cause -1/-1 counters to be placed on a creature with indestructible?

Wither is a keyword ability that changes the way a source deals damage to creatures. Instead of marking the creature with damage, the source places that many -1/-1 counters on the creature (CR 702.79b). This replacement effect applies to all creatures, including those with indestructible.

Indestructible (CR 702.12) means the permanent cannot be destroyed — it won't be destroyed by damage or by effects that say 'destroy.' It does not prevent counters from being placed on it, and it does not prevent damage from being replaced by counters. These are two completely separate game concepts.

The key distinction is that wither damage never actually 'damages' the creature in the traditional sense; it is replaced by counter placement before it ever registers as damage. Therefore, the creature does not die from lethal damage, but it still accumulates -1/-1 counters, reducing its toughness and power permanently.

Concrete example: Your opponent controls a 4/4 creature with indestructible. You attack with a 3/3 creature with wither. When the 3/3 deals its 3 damage, it is replaced by placing three -1/-1 counters on the indestructible creature, making it a 1/1. It will not be destroyed (indestructible protects it), but the counters remain, and if it ever reaches 0 toughness via additional counters, it is put into the graveyard as a state-based action (CR 704.5f), which is different from being 'destroyed.'

So yes, wither absolutely works on indestructible creatures — it just won't kill them through toughness reaching zero from a single hit unless enough counters accumulate to bring toughness to 0 via state-based actions.