I may have picked this up wrong , but you wish to use the CNC to drill the
holes. If this is the case then you should really create a drill file from
your cad package. This is normally a text file from which you could easily
extract the hole positions.
I don't think the drill positions are extractable from the gerber - except
by association with a flash code( aka aperture). How the pads are created
are very much at the behest of the cad package i.e. a large pad could be
flashed by a large flash aperture or it could be created by a smaller flash
which follows a path (a line of circles))
I would recommend trying to get the drill file first.

John

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