1. A controller, comprising: a memory that stores (i) a first model corresponding to a first critical dimension of a substrate processed by a substrate processing system and (ii) a second model corresponding to a second critical dimension of the substrate, wherein the second model includes a predicted relationship between the first critical dimension and the second critical dimension; and a critical dimension prediction module that (i) calculates a first prediction of the first critical dimension of the substrate using the first model, (ii) provides the first prediction of the first critical dimension as an input to the second model, and (iii) calculates and outputs a second prediction of the second critical dimension of the substrate using the second model.