[{name:"foo",fruits:{apple:{color:"green"},carrot:{color:"orange"},tomato:{color:"red"}}},{name:"no carrot",fruits:{apple:{color:"green"},tomato:{color:"red"}}},{name:"carrot only",fruits:{carrot:{color:"orange"}}}]

db.collection.update({},[{"$set":{"fruits":{"$filter":{"input":{"$objectToArray":"$fruits"},"as":"fruitKV","cond":{$eq:["carrot","$$fruitKV.k"]}}}}},{"$set":{"fruits":{"$arrayToObject":"$fruits"}}}])