We provide a framework for motivating and diagnosing the functional form in the structural part of nonlinear or linear structural equation models when the measurement model is a correctly specified linear confirmatory factor model. A mathematical population-based analysis provides asymptotic identification results for conditional expectations of a coordinate of an endogenous latent variable given exogenous and possibly other endogenous latent variables, and theoretically well-founded estimates of this conditional expectation are suggested. Simulation studies show that these estimators behave well compared to presently available alternatives. Practically, we recommend the estimator using Bartlett factor scores as input to classical non-parametric regression methods.