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Layers are incredibly important when using the Pen tool. There are four main tool functions of the Pen: creating paths, creating selections, creating masks and creating shapes. By default, you will draw paths. These live in the Paths palette and each appears on a new vector layer. These paths can be modified by Ctrl/right-clicking, or by selecting a new function from the top Options bar. Paths and layers exist independently of each other, so the order of one doesn’t affect the other. Just keep track of which layer you have selected.
To use a path to create a selection or a mask, have the path active and make sure the correct layer is selected. When drawing illustrations with shapes, layers are even more important. When you begin drawing with the Pen tool, always make sure you’re working on a new layer to avoid unwanted shape merging. Keeping the shapes on different layers allows for adjustments to be added, as well as changing layer order, which is useful for shading, adding backgrounds or extra details you may have forgotten about.