What it means
To scratch the surface is to deal with only the topmost, shallowest part of something, barely getting started on what lies beneath. You scratch the surface of a huge subject when you learn a few basics, or of a big task when you have done a tiny fraction. It usually comes with a sense of how much more there is still to uncover underneath.
Usage examples
"A weekend in the city barely scratches the surface of everything there is to see."
"We have only scratched the surface of what this software can actually do."
"We have barely scratched the surface of what this little gadget can actually do."
"That documentary only scratches the surface, it never digs into the real story."
"Mate, we've only scratched the surface here. The proper mess is still underneath."
Where it comes from
A transparent image: if you only scratch the very top of something you barely mark it and never reach what lies underneath, so the phrase means dealing with just the shallowest part and leaving the real depth untouched.