A metrology system includes an image device and a controller. The image device includes a spectrally-tunable illumination device and a detector to generate images of a sample having metrology target elements on two or more sample layers based on radiation emanating from the sample in response to illumination from the spectrally-tunable illumination device. The controller determines layer-specific imaging configurations of the imaging device to image the metrology target elements on the two or more sample layers within a selected image quality tolerance in which each layer-specific imaging configuration includes an illumination spectrum from the spectrally-tunable illumination device. The controller further receives one or more images of the metrology target elements on the two or more sample layers generated using the layer-specific imaging configurations. The controller further provides a metrology measurement based on the one or more images of the metrology target elements on the two or more sample layers.