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I think I understand what you mean. Though if you could somehow visualise it I would understand even better. What I would do I think, is make a 3D part that is "popped" onto the PCB and which also hooks behind the tab on the PCIe Socket. To remove it you "pop" the hook out. Down-side would be that it's a small part and easily lost.




I see what you mean, that would add a little thickness, but customizing would greatly improve.

The top part should be okay as is, but I'll have to add a small lip to have the PCB go past the socket, currently it would be flush with the socket.

is 1mm the minimum thickness for 3D printing?