Alignment of a near field transducer (NFT) optical input coupler and a light emitting device involves providing excitation radiation from an excitation light source through an optical input coupler to the NFT and filtering output radiation from the NFT using a short wavelength pass optical filter. The optical input coupler is scanned through multiple positions while the photoluminescent radiation is detected. A first alignment position between the NFT input coupler and the excitation light source is identified based on the detected photoluminescent radiation. A light emitting device is scanned through multiple positions the light output is detected by a detector. A second alignment position between the light emitting device and the detector is identified. The first and second alignment positions are used to align the light emitting device with the optical input coupler.