Database

[{"_id":"612d0ba09403d0224b55cb6d","nickname":"tester","email":"test@test.com","password":"tester","characters":[{"id":0,"name":"hdfghgfd","skin":"thor","exp":0,"account_id":"612d0ba09403d0224b55cb6d"},{"id":1,"name":"bdfsgfds","skin":"starlord","exp":0,"account_id":"612d0ba09403d0224b55cb6d"}]}]

Query

db.collection.update({_id:"612d0ba09403d0224b55cb6d"},{"$pull":{"characters":{"id":0}}})

Result