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Every layout consists of several layers that can be used independently or treated as a group. Layer groups can be used to logically separate (and color-code) different traces (e.g. power and signal); however, all layers within a group reside on the same physical copper layer of a board, so using different layers within the same group won't provide electrical separation where they touch or overlap. For details, see ‘layerGroups’, Resources. Each layer is drawn in a color defined in the resource file and identified by a name that you can change (for details see ‘layerColor’, Resources.) Layers are really just containers for line, arc, polygon, and text objects. The component and solder layers contain SMD elements as well, but the file structure doesn't reflect that fact directly.

Each layer group represents a physical layer on the printed circuit board. If you want to make a four layer board, you'll need to have at least four layer groups. Connections between layer groups are established only through element pins and vias. The relationship between a specific layer and the board itself is configurable from the ‘Edit layer groups’ option in the Settings menu. The layer groups corresponding to the physical layers: component-side and solder-side are always defined and you must map at least one logical layer to each, even if you plan to make a single-sided board. You are not obligated to put tracks on either of them. Surface mount elements always reside on either the component-side or the solder-side layer group. When you paste an element from the buffer, it will go onto whichever side of the board you are viewing. You can swap which side of the board you are viewing by pressing the Tab key, or by selecting ‘view solder side’ from the Screen menu. The layer groups just have a name or number associated with them - where they are sandwiched in the board is left for you to tell the manufacturer.

The silkscreen layer is special because there are actually two silkscreen layers, one for the top (component) and one for the bottom (solder) side of the board. Which silk layer you draw on is determined by the side of the board that you are viewing. If you are viewing the component side, then drawing on the silk layer draws to the component-side silk layer.

The netlist layer is another special layer. It shows rat's-nest lines (i.e. guides that show how the netlist expects the element to interconnect). If you make this the active layer, you can use the Line tool to add entries into the netlist, or to delete connections from the netlist window. Except for these two purposes, you should not make the netlist layer the active layer. Usually there is no need to do this because a separate schematic package should be used to create the netlist. Pcb can automatically draw all of the rats from the netlist. In some cases you may want to make a small change without going to the trouble of modifying the schematic, which is why this facility is provided.