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For security reasons, how can I scrub customer data on gerber files?

In general, this simply involves deleting logos, names, etc on the silkscreen layers.

1. Load Gerbers: 
A. If they're zipped, then use menu:  File | Import | Zipped (Compressed File)... 
B. If they're in a folder, then use menu:  File | Import | Autoload...   (and select the folder where the gerber files for a pcb exist). 

Note: FAB 3000 will automatically load in your gerbers & drills. 

2. Once you find the customer data you want scrubbed, select those objects (goto menu: Edit | Selection) and then Delete (menu: Edit | Delete).  
Note:  Both of these options can be access by using Rt-Click menu. 

3. Export new fresh set of gerber files.  File | Export | Gerber... 

Note: Make sure to export to a different folder, and then send those file out

There are two protection advantages: 
A. The customers information is no longer displayed in the gerbers. 
B.  Most gerber files contain hidden information about the designer & their design software used (look at your gerber files in a simple text viewer like notepad.exe to prove tis point). Gerber files outputted from FAB 3000 will not include any hidden information about your designer & CAD system. 
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