We cut stencils all the time with our lasers out of laser transparency.
Kapton does not work as well as mylar. Several people have recommended Kapton without trying it. Our first hand experience indicates it is inferior to laser transparency.
You need to raster the image. Vector cutting doesn't work well to produce nice even holes.
We can easily raster cut holes for .5mm pitch devices with our CO2 lasers. We rastered all the stencils for our RetinaEngrave prototypes and hand assembled them under a microscope.
I would say .1mm holes are beyond the normal diffraction limit of CO2.
Full Spectrum Engineering