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I want to know for physical comparison options, what is the normal minimum error size. 4 mi, 10 mils. What is the std?

As a general rule the smaller the error size (i.e .tolerance), the longer physical comparison will take.

The error size is a variable, because there are many unique reasons for performing a physical compare.   There isn't any specific standard for comparison.   

If checking between PCB design versions, probably setting to 4 mils tolerance would be fine.  Typically in these cases, the designer is looking for the changes between layouts (which is typically significant - like adding a different component., re-routing traces, etc.).

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