Hey, My MacBook is doing the same thing! Its like a scratching noise for me and happened 4 days ago and happened briefly a few minutes ago, since then i've been searching the web wondering why, this is what i found so far:
Sometimes, when a hard drive is failing or about to fail, it can make those kinds of grinding noises. It’s a precursor to something much, much worse. Internal destruction is usually what’s next.
That grinding noise is something loose inside the hard drive, where there simply shouldn’t be anything loose. That typically means that when that thing becomes completely loose, it’s going to go flying around in there and cause all sorts of destruction within the drive itself.
Though, it could be the fan, i am terribly scared. Did you fix it, by the way? If so, what was it?