M101JS 3.1

app.js

var mongo = require('mongoskin');
var _ = require('underscore')._;
var db = mongo.db('mongodb://localhost:27017/school');

var collection = db.collection('students');
var cursor = collection.find();

cursor.each(function(err, doc) {
	if (!doc) return;

	console.log("\n" + '-------START of document-------' + "\n");

	console.log("doc:", doc);

	var homework = _.sortBy(_.filter(doc.scores, function(score) {
		return score.type === 'homework'
	}), 'score');

	var lowestScore = homework[0];

	console.log("homework scores:", homework);
	console.log('lowest homework score: ', homework[0]);

	if (lowestScore) {
		collection.update({ _id: doc._id}, { '$pull': { scores: { type: 'homework', score: lowestScore.score }}});
	}

	console.log("\n" + '-------END of document-------' + "\n");
});

console.log('starting....');

Even if this is not the best way, it works :)