A dental laser treatment system includes a treatment laser beam and a pilot (e.g., aiming/marking) laser beam sharing a collinear beam path, where the beam path is guided by a guidance system through a handpiece/main chamber assembly having a beam exit. A laser beam presence detector is removably affixed to or within the handpiece/main chamber assembly. The laser beam presence detector provides feedback to a computer which can control actuation of the treatment laser beam and the pilot laser beam, and the beam guidance system. The computer performs a search for determining the center location of the beam exit based on the feedback and controls the beam guidance system to guide the beam path approximately to the center of the beam exit, thereby providing automatic alignment of the laser beam with the beam exit or an optional hollow waveguide.
