Methods for controlling lithographic apparatus, lithographic apparatus and device manufacturing method

A non-transitory computer program product comprising machine readable instructions therein, the instructions configured, upon execution by a data processing apparatus, to cause the data processing apparatus to at least:

• obtain height sensor data representing a topographical variation across a substrate;
• identify one or more first areas of the substrate where the height sensor data is judged to be reliable and one or more second areas of the substrate where the height sensor data is judged to be less reliable;
• determine substitute height data for the one or more second areas using the height sensor data for the one or more first areas together with prior knowledge of expected device-specific topography that specifies a height difference between a first area and a neighboring second area;
• and
• control a lithographic apparatus using a combination of the height data and the substitute height data for applying a device pattern at a location on the substrate.

A non-transitory computer program product having machine readable instructions therein, the instructions configured, upon execution by a data processing system, to cause the data processing system to at least:

• obtain height sensor data representing a topographical variation across a substrate;
• identify one or more first areas of the substrate where the height sensor data is judged to be reliable and one or more second areas of the substrate where the height sensor data is judged to be less reliable;
• enhance height sensor data for one or more first areas by deconvolution of that data with a height sensor response function;
• determine substitute height data for the one or more second areas using the enhanced height sensor data for the one or more first areas;
• and
• control the lithographic apparatus using a combination of the height data and the substitute height data for applying a device pattern at a location on the substrate.