KB: Create a default footprint with the layers specified

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1. If the template will be used locally: 
Use File » New » Library and select PCB Library from the options: »

Hit the key L (for View Configuration) and define layers you want to use in the template.
You can change the colors, add component layer pairs, add mechanical layers and so on.

Then save the PCB Library (.PcbLib) somewhere on the PC.

After that go to Preferences » Data Management » Templates » [Defaults] » [Add...] and in the drop down menu select From File, navigating to the saved .PcbLib file. Then hit ok. Now the creation of the new footprint will follow the template.

 

2. If the template will be used in A365: 
Open Explorer panel and navigate to Managed Content » Template folder:

 

Use the Upload... option if the template has been defined and saved locally already. Then use the Add button to navigate to it. After the pcbLib file has been selected hit the OK button to close the dialog.

Use Create Item... » Footprint if the footprint template was not created yet. Give it a name and description if needed in the next dialog: 

In the Footprint Editor hit the L button to open the View Configuration panel. Now set up the layers you want to use in your footprint template and hit OK. Then go to File » Save to Server. Add release notes if needed and hit Ok.

The footprint template has been created and is saved on the server waiting to be set up as a template.

For that, go to Preferences » Data Management » Templates » [Defaults] » [Add...] and use the option From Server » Footprint. This will automatically open the Explorer panel showing the available footprint template(s).

Select one and hit OK. 

From now on, the creation of a new footprint from scratch or using the Footprint Wizard will follow the predefined footprint template.