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I am trying to subtract elements from Layer 1 from elements from Layer 2 to create holes in Layer 2 that match the elements in Layer 1. I can use the Boolean Subtract function for individual objects, but I cannot select multiple (all) objects from Layer

There are two options.

1. Build Composite (menu:  Tools / Composites / Build Composite...)

2. Boolean Wizard (menu:   Tools / Boolean Wizard / Subtract...).

Build Composites is actually the preferred way to perform boolean subtraction on your design - instead of Boolean Wizard.  Here's a movie showing how to perform that command, 

Note:  Boolean Wizard converts everything to polygons and then performs the subtracting - which can result in massive polygons with cutlines.

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