A method for aligning a beam spot with a waveguide portion of a wavelength conversion device includes scanning a beam spot over the input face of the wavelength conversion device while measuring the output intensity of the device such that an output intensity for each of a plurality of fast scan lines is generated. A first alignment set point is then determined based on the output intensity of each fast scan line. A second scan of the beam spot is then performed over the fast scan line containing the first alignment set point while measuring the output intensity for each point along the fast scan line. A second alignment set point is then determined based on the output intensities measured during the second scan. The beam spot is then aligned with the waveguide portion using the first alignment set point and the second alignment set point.