Does an effect that sets a creature's power and toughness to a specific number override +1/+1 counters?

Magic resolves power/toughness modifications in a specific sequence called the "layer system" (CR 613). Layer 7 handles power and toughness, and it is divided into sub-layers that are always applied in order regardless of timestamp.

Effects that set a creature's power and/or toughness to a specific value (e.g., "becomes a 3/3") apply in layer 7b (CR 613.3b). Effects that add or subtract from power/toughness apply in layer 7c. Counters such as +1/+1 counters are applied in layer 7d (CR 613.3d).

Because layer 7d always comes after layer 7b, a +1/+1 counter on a creature will always be counted on top of whatever a setting effect established. The setting effect does not "erase" the counter — the counter is simply added afterward in the calculation.

Example: You control a Runeclaw Bear (normally 2/2) that has one +1/+1 counter on it. An opponent casts an effect that turns it into a 3/3 until end of turn. The 3/3 setting applies in layer 7b, then the +1/+1 counter adds 1/1 in layer 7d, making the bear a 4/4 until end of turn.

This is true even if the setting effect has a later timestamp than when the counter was placed. The sub-layer ordering is mandatory and always overrides timestamp order within layer 7 (CR 613.3).