Hi @01xDaniel ,
I hope you're doing well. That is a good question and there are many ways to address it. IMO, the most foolproof way is to add an attribute in the BOM of called something like Do Not Place. Then for each component type Yes or No.
Talk to your board manufacturer and ask them how they want that information called out and conform to that.
Let me know if there's anything else I can do for you.
Best Regards,

Jorge Garcia
Product Support Specialist for Fusion 360 and EAGLE
Kudos are much appreciated if the information I have shared is helpful to you and/or others.
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