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Clearance denotes the shortest distance between two conductive parts as measured through the air.

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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' Constraints … : Min Vertical Clearance 0mil Min Horizontal Clearance 0mil Then Altium Designer will not check this component's clearance. …
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