I have a collection with a following data:
{ \"_id\" : ObjectId(\"4e3951905e746b3805000000\"), \"m\" : \"hello\", \"r\" : [{ \"_id\" : ObjectId(\"4e
It's easy, you just need to use $pull operator:
db.items.update( {}, { $pull : { r : {"_id": ObjectId("4e39519d5e746bc00f000000")} } }, false, false )