Actually, you'd want the clear to be applied to as smooth a surface as possible. Underlying scratches get magnified (or at least to the eye they appear more exaggerated) by clear coat. The clear should adhere just fine to a glass smooth surface. The difference here between what a polish does and what clear does is that the polish fills the fine scratches with an opaque substance that hides them. Over time it washes out and the scratches seem to re-appear. With clear, you'd fill them with a clear substance which would hold up to washes and wear much longer, but would show those scratches. You can see this in re-paints on cars often. If the primer was not sanded with a fine enough paper, or if it was used as a filling primer and subsequently shrinks some, you'll see scratches in the underlying primer, through the clear coat.