Soul-Scar Mage has a replacement effect: if a spell you control would deal damage to a creature, that damage is instead prevented and that many -1/-1 counters are placed on the creature. This conversion happens before any damage-based destruction is considered.
Indestructible (CR 702.12) means a permanent cannot be destroyed by effects that say 'destroy' and is not destroyed by lethal damage (CR 704.5g). It does NOT protect against -1/-1 counters reducing a creature's toughness to 0 or less, which causes the creature to die via state-based actions under CR 704.5f instead.
Because Soul-Scar Mage's effect is a replacement effect (CR 614.1), the damage never actually occurs — counters are placed instead. Since indestructible only blocks 'destroy' effects and lethal-damage destruction, it offers zero protection against a creature's toughness being reduced to 0 by -1/-1 counters.
Concrete example: You control Soul-Scar Mage and cast Lightning Bolt targeting your opponent's indestructible Darksteel Myr (0/1). Instead of dealing 3 damage, three -1/-1 counters are placed on it, making it a 0/-2. State-based actions then see its toughness is 0 or less (CR 704.5f) and it is put into the graveyard — indestructible does not save it.
In short, Soul-Scar Mage is one of the best answers to indestructible creatures precisely because it sidesteps the destruction mechanism entirely.
Unofficial fan resource — not affiliated with or endorsed by Wizards of the Coast. Answers are AI-generated estimates grounded in the Comprehensive Rules and are not a substitute for an official judge. Verify anything match-critical.