Disclosed are a method, computer program and a metrology apparatus for measuring a process effect parameter relating to a manufacturing process for manufacturing integrated circuits on a substrate. The method comprises determining for a structure, a first quality metric value for a quality metric from a plurality of measurement values each relating to a different measurement condition while cancelling or mitigating for the effect of the process effect parameter on the plurality of measurement values and a second quality metric value for the quality metric from at least one measurement value relating to at least one measurement condition without cancelling or mitigating for the effect of the process effect parameter on the at least one measurement value. The process effect parameter value for the process effect parameter can then be calculated from the first quality metric value and the second quality metric value, for example by calculating their difference.