[{"id":1,"instances":[{"id":2,"owner":{"id":2}}]},{"id":2,"instances":[{"id":1,"owner":{"id":1}},{"id":4,"owner":{"id":2}}]},{"id":3,"instances":[{"id":3,"owner":{"id":1}}]}]

db.collection.update({},{$pull:{instances:{"owner.id":1}}},{multi:true})