Let's understand your vehicle's paint and how it works.

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When vehicles first started being produced, the metal panels were covered in a thin coat of paint to protect them from rust and decay.  Over time this protective coating now known as the base or color coat became available in different colors which consumers took to give their ride a customized look. As time went on, the thin base coat would become damaged or faded leaving behind a dull and not so beautiful finish that would need to be repainted.  Introduce the clear coat. Clear coat was developed as a clear layer to protect the base coat from becoming sun-faded or damaged. Although still thin, this clear coat is thicker than the base coat and takes the brunt of the beating. In order for the base coat and clear coat to adhere to the body panel, a layer of primer is applied. 

As pictured above, most scratches and defects you see in your vehicle's paint are actually in the clear coat which can typically be fixed via machine polishing.  Only deep scratches tend to go through the base coat, and some all the way through the primer to the body panel. These deeper scratches will need to be touched up or repaired. 

To recap, the primer allows the base coat to bond to the body panel. The base coat protects the body panel and the clear coat protects the base coat.