An autofocus system and method designed to account for instabilities in the system, e.g. due to instabilities of system components (e.g. vibrating mirrors, optics, etc) and/or environmental effects such as refractive index changes of air due to temperature, atmospheric pressure, or humidity gradients, is provided. An autofocus beam is split into a reference beam component (the split off reference channel) and a measurement beam component, by a beam splitting optic located a predetermined distance from (and in predetermined orientation relative to) the substrate, to create a first space between the beam splitting optic and the substrate. A reflector is provided that is spaced from the beam splitting optic by the predetermined distance, to create a second space between the reflector and the beam splitting optic. The measurement beam component is directed at the substrate and a reflected measurement beam component through the first space between the substrate and the beam splitting optic, while the reference beam component is directed at the reflector and a reflected reference beam component is directed from the reflector through the second space between the beam splitting optic and the reflector. The reflected reference and measurement beam components are returned to the beam splitting optic, and emerge substantially collinear from the beam splitting optic. The reference and measurement beam components are then detected, and provide information that enables compensation for changes in the z position of the substrate that are due to instabilities in the autofocus system components and/or environmental factors.