Clear will fill! If you use a gray 3m scuff pad or 1200 grit sandpaper. For example, when blending, you sand the surface to be cleared with a gray scuff pad or 1200 grit sandpaper. When you clear the area it will fill the scratches and produce a nice quality finish.
The problem with sanding base: is that you can discolor the metallic or sand through easy. That is why I would suggest using a mid-coat clear after spraying your base. This is just a base coat that is clear. The PPG number is 500. Therefore, the clear will fill the scratches, but will not cover sand through or discolored areas. If it is a solid color you should be fine.
What color are you shooting? Is it a metallic or pearl? That will help.
Thanks, Donnie