Layers allows increased flexibility whilst retouching and the ability to create complex digital photomontages. Layers are like a series of acetate sheets, each with a different part of the image, stacked on top of each other. The classic Walt Disney animations were created using this versatile imaging technique. Each character can be placed on their own acetate sheet so that when the character is moved the background does not have to be continuously redrawn.

Parts of a layer may be transparent allowing information on the layers underneath to be visible. At the bottom of the stack is the background layer which remains opaque. The layers can be rearranged so that pixels may be brought forward or concealed behind the pixels on the layers above. Layers are controlled via the layers palette and layers menu.