Like FiberGeek said, the only process that will really 'scrap' a part is the stripping process, assuming you're using standard anodizing or the LCD method.
I have tried to measure the thickness of an anodized layer, as I have heard that it does change the dimensions slightly. However, I do not have the measurement tools necessary. I have never seen a change that was measureable with a pair of calipers good to 0.001". I would imagine that if your tolerances are +/-0.001" or larger, you will have no problems.
Also, there are ways to mask areas that you do not wish to be anodized.
Hope it helps!
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