The authors report the principle and experimental observation of fluorescence moiré interference fringes for alignment in the print and imprint methods. Concave bar and cross alignment marks on a silica mold and substrate without the deposition of any light-shielding or high-refractive-index layers could be visualized by fluorescence microscopy with a fluorescent liquid sandwiched between the patterned surfaces. Fluorescence moiré interference fringes with a pitch of 44 μm were generated by the superimposition of two sets of mold bar arrays with respective pitches of p1 = 4.0 μm and p2 = 4.4 μm on substrate bar arrays with different periodicity of p2 and p1 through a thin fluorescent liquid layer. The fluorescence moiré fringes were attributed to an additive-type generation by the interference of two luminous gratings with different periodicities, which was different from a multiplicative-type generation by the superimposition of two light-shielding metal gratings with different periodicities under illumination. Coarse alignment with 2-μm-wide cross marks was performed by manually operating the substrate-side stages, and the misalignment was evaluated with the two sets of fluorescence moiré fringes. The alignment method by fluorescence microscopy with a fluorescent liquid provided the possibilities of not only fine alignment with fluorescence moiré fringes but also in situ monitoring of the residual layer thickness formed between the mold and substrate surfaces before curing for ultraviolet nanoimprinting.