A methodology is provided for correcting the placement of a laser beam's focal point. Specifically, this correction is done to compensate for displacements of the focal point that may be caused when implant material (e.g. an Intraocular Lens (IOL)) is positioned on the optical path of the laser beam. The methodology of the present invention then determines a deviation of the laser beam's refracted target position (uncompensated) from its intended target position. A calculation of the deviation includes considerations of the laser beam's wavelength and refractive/diffractive characteristics introduced by the implant material. This deviation is then added to the refracted target position to make the refracted target position coincide with the intended target position of the focal point. The laser beam will then focus to its intended target position.