XSL customization layers are XSL files that import XSL formatting instructions from a base or default set of instructions and then replace, modify, or augment the imported instructions. Mr. XML Publisher will format projects using the XSL customization layers they contain; however, Mr. XML Publisher will do so only if the name of the file containing the main XSL customization layer is the same as the name of the project's main XML file, but with a ".xsl" extension.

When an uploaded project does not contain an XSL customization layer, or does not contain a correctly named XSL customization layer, Mr. XML Publisher uses the default XSL for the chosen format as defined in the format's command array. The default XSL may itself be a customization layer that imports XSL. For a discussion of a format's default XSL and XSL customization layers, see XSL and Customization Layers.