The present disclosure relates to a semiconductor device and a manufacturing method, and more particularly to a semiconductor device having self-aligned isolation structures. The present disclosure provides self-aligned isolation fins that can be formed by depositing dielectric material in openings formed in a spacing layer or by replacing portions of fins with dielectric material. The self-aligned isolation fins can be separated from each other by a critical dimension of the utilized photolithography process. The separation between self-aligned isolation fins or between the self-aligned isolation fins and active fins can be approximately equal to or larger than the separations of the active fins.