...but the problem is that I think it creates a whole bunch of little cubes, building a solid representation of the matrix. What I need is just a skin of the solid that would be created by this method...
I think you're mistaken. The marching cubes method creates an isosurface, so a "skin" like you say, that represents the 2D exterior surface of the model. It only creates polygons in areas that share empty space and filled space.
Also, even if it's called "cubes", it doesn't just create cubes like, say,
my trixel engine.

It actually tries to mimic the curves of the model by using 15 possible cube configurations, that map to different polygon generation cases.
The screenshot on wikipedia uses flat shading, which makes it look pretty rough, but with vertex normals or phong shading it can generate very smooth/organic models.