Predictive modeling based focus error prediction method and system are disclosed. The method includes obtaining wafer geometry measurements of a plurality of training wafers and grouping the plurality of training wafers to provide at least one training group based on relative homogeneity of wafer geometry measurements among the plurality of training wafers. For each particular training group of the at least one training group, a predictive model is develop utilizing non-linear predictive modeling. The predictive model establishes correlations between wafer geometry parameters and focus error measurements obtained for each wafer within that particular training group, and the predictive model can be utilized to provide focus error prediction for an incoming wafer belonging to that particular training group.