A lithographic apparatus includes a number of sensors for measuring positions of features on a substrate prior to applying a pattern. Each sensor includes an imaging optical system. Position measurements are extracted from pixel data supplied by an image detector in each sensor. The imaging optical system includes one or more light field modulating elements and the processor processes the pixel data as a light-field image to extract the position measurements. The data processor may derive from each light-field image a focused image of a feature on the substrate, measuring positions of several features simultaneously, even though the substrate is not at the same level below all the sensors. The processor can also include corrections to reduce depth dependency of an apparent position of the feature include a viewpoint correction. The data processor can also derive measurements of heights of features on the substrate.