<p>Alignment accuracy of micropatterns is a critical factor affecting the performance of products in industrial applications. In multilayer structures, where patterns of different shapes must be precisely superimposed, even slight misalignments can significantly degrade performance, necessitating high-precision alignment. Conventional alignment techniques rely on alignment marks, which require additional fabrication processes to preserve mark quality, leading to increased manufacturing costs and a reduced effective pattern area. In this study, we propose a Fourier transform-based alignment technique that enables precise alignment of differently shaped patterns without the use of alignment marks. The proposed method quantitatively analyzes and corrects rotational misalignment by comparing the Fourier spectrum of a perfectly aligned reference pattern with that of a target pattern. Leveraging the rotational invariance and linearity properties of Fourier transform analysis, we experimentally verified that the proposed approach can accurately evaluate and correct alignment offsets between rotated patterns. This method overcomes the limitations of conventional alignment techniques and presents a promising alternative for implementing more efficient alignment processes across various industrial fields, including semiconductors, displays, and printed electronics. It can be effectively applied to the alignment of microlens arrays (MLAs) with patterned substrates in optical security films, the registration of Color filters with thin-film transistors (TFTs) in high-resolution display panels, and the alignment of gate and source–drain electrodes in TFT structures, as well as driving and sensing electrodes in touchscreen panels. This approach simultaneously addresses the challenges of geometric diversity and markless processing, positioning itself as a key enabler of next-generation precision manufacturing technologies.</p>