var userSchema = new Schema({
field: {},
field2: {},
field3: {
    innerField1: String,
    innerField2: String,
    innerField3: String,
    innerField4: String,
    innerField5: String,
    innerField6: String
}
});

{
   field3: {
      innerField2: String,
      innerField4: String
   }
}

Schema.findOneAndUpdate({_id: userId}, {$set: req.body.field3}, function(err, res) {});

Schema.UpdateById(userId, {$set: req.body.field3}, function(err, res) {});