A lithographic apparatus and method are used for manufacturing a device. A projection system is configured to project a patterned radiation beam onto a target portion of the substrate. A Higher Order Wafer Alignment (HOWA) model is applied so as to model higher order distortions across the substrate. The model is applied using at least one input parameter for which at least one intra-field effect has been taken into account. In an example, the intra-field effect taken into account is the ScanUp-ScanDown effect and/or the ScanLeft-ScanRight effect.