A method of registering and vertically aligning multiply-layered images into a mosaic is described. The method comprises performing an iterative process of vertical alignment of layers into a mosaic using a series of defined alignment correspondence pairs and global registration of images in a layer using a series of defined registration correspondence points and then redefining the identified alignment correspondence pairs and/or registration correspondence points until a satisfactory result is obtained. Optionally, an initial global registration of each layer could be performed initially before commencing the alignment process. The quality of the result could be determined using a least squares error minimization or other technique.