You need to sand the paint around the scratch until the scratch is gone. You'll likely have a 4 inch area of sanded and feathered out paint around where the scratch was. Be sure each layer (metal, e coat/primer, color, clear)is at least a 1/4-1/2 an inch visible, assuming there's been no other paint work on the area.

Prime it. Block the primer. Sand the entire panel. Blend color out from the repair area, if the repair is close to an adjacent panel you'll have to blend the color into the adjacent panel as well if you want it to match and it not be visibly off. Then clear coat it. You only need to wet sand the clear if it looks bad. Which it will if this is your first attempt at something like this.

Depending on the paint system you are using you'll need sand paper in grits ranging from 180-220-400-600-800-1500-2000.