I am building a laser machining setup.  The setup consists of a laser
(800 nm) entering a 2x beam expander (Galileo type) then passing
through a dichoric mirror and then into a microscope objective lens
(100x) to be focused on to the sample.  The dichoric mirror reflects
visible light coming out of the microscope objective into a beam
splitter.  The beam splitter reflects white light from a lamp back
toward the dichoric mirror and down in the objective to illuminate the
sample.  The beam splitter transmits the light from the objective into
a CCD camera.

The sample to be machined sits on an XYZ stage underneath the
microscope objective.  The correct operation of the setup will be to
bring the surface of the sample in focus by viewing the video from the
CCD. When the surface of the sample is in focus in the CCD, the laser
will be focused exactly at the surface of the sample, and from there
the sample will be moved to preform machining.

In order to  machine precise holes to a certain depth, the initial
focus is key so that it is known the laser starts at the surface and
the sample needs to be translated the desired depth of the hole.

I have found that in my setup, the focus of the laser and focus seen
in the CCD image are not the same.  In other words, when the sample is
in focus in the video monitor, the laser focus is not at the surface
of the sample.  From trial and error, it is found to be a small
distance above the surface sample.

My question is how can I accurately match the foci of the imaging and
laser optics so that when the surface is in focus in CCD, the laser is
focused precisely at the surface of the sample.

Change the axial position of the CCD camera till the two images are at
the same focus.

By the way, I wouldn't use a 100x objective.  What you need is a high
NA objective.  Magnification is not relevent (or useful) for imaging
the laser.  If you need higher magnification for your camera use
auxilliary optics in the camera path.