You can use caulking to patch the holes, or fill with Bondo from the automotive stores and sand the siding smooth. Since you're dealing with very small and somewhat rough holes, Bondo, and even caulking, is heavy enough to sit in the hole in the aluminum where it can dry and then can be sanded flush with the siding. For larger holes in siding, you may need to span the area with mesh tape and apply Bondo over this, similar to a drywall butt seam.
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