Is there any method for ModifiedComponent.Apply()?

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Well, the PrefabUtility should contain everything you need. Specifically look at ApplyObjectOverride, ApplyPrefabInstance and ApplyPropertyOverride. They have different usecases, so make sure you read the description carefully. When you design an editor tool, make sure you test it on a duplicate / backed up project.

I don’t think so but why would you need it? You could just do it by right-clicking and applying it…