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Printed Circuit Boards (PCBs) are composed of a sandwich of alternating layers of insulating substrate and conducting copper layers. The copper layers are etched to form connecting tracks between components as well as earth/ground or power planes. The simplest PCB has one substrate layer and one copper layer. Generally only the copper layers are counted. A complex PCB might have seven layers.

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How do I disable clearance check for a layer or for only some certain elements?

You can specify a design rule for that component: Design > Rule > Placement > Component Clearance, Add new rule like this: Advanced query: InComponent('D1') //assume the component is 'D1' …
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