John,
     I have set up 2 such solder paste measurement systems.  One at my
previous employer and now one at my new employer.  In both cases I choose
the Alpha Hi-check system over the Cyberoptics unit.  But, regardless of
the equipment you should try to measure to the pad surface.  If you are
undercutting you stencils at all (most do) you will have some exposed pad
to measure to.  This will give you your truest number as far as the actual
thickness goes.  In experiments where I did not have any stencil reduction
I would measure pad height from substrate, then print, then measure
substrate to paste and find the difference.  But in production we use the
edge of the pad from the stencil reduction to the paste.  We measure 5
locations on a board: all 4 corners and the center- however if BGA or fine
pitch is used those are measured.  We measure the 3rd piece of each run
(not the first of second because of paste kneading), and the again at the
mid point of the run.

     If you are using organic coating instead of HASL and are not worried
about the true paste thickness you could measure from the substrate to the
paste.  The copper should be consistent enough to give you the consistency
you need.  This will allow you to track the consistency of the paste
printing process, just not necessarily the true paste thickness.  My
recommendation is to use the actual pad surface if at all possible.

Good luck,
Brad Kendall

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