As you can see all of the enclosures in my project have holes (for the USB, LAN, Antenna or GPIO connectors).

I did some special tools which allow me to cut holes with good precision and repeatability. 

It's also saving me a huge amount of time. Because after installing the fixing tool I can quickly change the enclosures for milling.

You can see the whole process on video:

Timeline:
0:00 Tool for fix the enclosure for the side holes milling
0:10 Setting XY zero by the template
0:17 Changing the template to the new enclosure 
0:35 Setting Z and side holes milling
1:16 Changing fixing tool for USB and LAN holes milling
1.36 Setting XY zero by the template
1:43 LAN hole milling
2:30 USB holes milling
2:53 Changing fixing tool for the antenna hole milling
3:10 Setting zero and the antenna hole milling

Final result: