Disclosed is a system and associated methods for generating a composite image from scans or images that are aligned using invisible fiducials. The invisible fiducial is a transparent substance or a projected specific wavelength that is applied to and changes reflectivity of a surface at the specific wavelength without interfering with a capture of positions or visible color characteristics across the surface. The system performs first and second capture of a scene with the surface, and detects a position of the invisible fiducial in each capture based on values measured across the specific wavelength that satisfy a threshold associated with the invisible fiducial. The system aligns the first capture with the second capture based on the detected positions of the invisible fiducial, and generates a composite image by merging or combining the positions or visible color characteristics from the aligned captures.