If you want to work with layers in your diagrams but always want to keep a visible base structure, you should combine layers with our new background page feature. To learn more about layers, check out our playlist at https://drawio.link/layers. How to use layers with interactive button navigation can be found at https://drawio.link/interactive.
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Or learn more about diagramming with draw.io at https://drawio-app.com/learning. You can also take a look at our blog (https://drawio-app.com/blog) to always stay up-to-date on new draw.io features in Confluence.