very basic cad cam software

[Clive S]

This is the bit I don't understand, why make the hole bigger if a 3mm hole is required ? Sometimes this will be fine but I'm sure there are more instances where the measurement has to be right.

The way I see it is If you want the hole to be 3mm and you also want to profile it out then you have to use a smaller end mill say 2.5mm BUT if you have a job like Charlie is doing and he is wanting to use a 3mm end mill to do the total job and the 3mm hole size does not have to be 3mm then make it say 3.01 and use the same cutter to save changing bits (his holes are only for mounting holes anyway).
I did a very similar job for a quadcoptor all with one size bit and did the same just made the 3mm holes to 3.01.
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Or like has already been suggested peck drill it