In the a official mongoose site I\'ve found how can I remove embedded document by _id in array:
post.comments.id(my_id).remove();
post.save(function (err) {
Update to latest docs on dealing with sub documents in Mongoose. http://mongoosejs.com/docs/subdocs.html
var Parent = mongoose.model('Parent');
var parent = new Parent;
// create a comment
parent.children.push({ name: 'Liesl' });
var subdoc = parent.children[0];
console.log(subdoc) // { _id: '501d86090d371bab2c0341c5', name: 'Liesl' }
subdoc.isNew; // true
parent.save(function (err) {
if (err) return handleError(err)
console.log('Success!');
});