A metrology system comprising: A metrology tool; and a controller including one or more processors configured to execute instructions configured to cause the one or more processors to: generate a three-dimensional model of a sample including one or more instances of a structure to be analyzed by the metrology tool; generate one or more predicted metrology images corresponding to a predicted analysis of the sample with the metrology tool based on the three-dimensional model, wherein the predicted metrology image includes predicted deviations from a two-dimensional projection of the three-dimensional model based on the predicted analysis of the sample with the metrology tool; evaluate two or more candidate metrology recipes for extracting a metrology measurement from the one or more predicted metrology images; select, based on one or more selection metrics, a metrology recipe from the two or more candidate metrology recipes for extracting a metrology measurement from an image of the structure from the metrology tool; receive, from the metrology tool, an output metrology image of a fabricated structure based on a metrology measurement of the fabricated structure; and extract the metrology measurement associated with the fabricated structure from the output metrology image based on the metrology recipe. A metrology tool; and a controller including one or more processors configured to execute instructions configured to cause the one or more processors to: generate a three-dimensional model of a sample including one or more instances of a structure to be analyzed by the metrology tool; generate one or more predicted metrology images corresponding to a predicted analysis of the sample with the metrology tool based on the three-dimensional model, wherein the predicted metrology image includes predicted deviations from a two-dimensional projection of the three-dimensional model based on the predicted analysis of the sample with the metrology tool; evaluate two or more candidate metrology recipes for extracting a metrology measurement from the one or more predicted metrology images; select, based on one or more selection metrics, a metrology recipe from the two or more candidate metrology recipes for extracting a metrology measurement from an image of the structure from the metrology tool; receive, from the metrology tool, an output metrology image of a fabricated structure based on a metrology measurement of the fabricated structure; and extract the metrology measurement associated with the fabricated structure from the output metrology image based on the metrology recipe. generate a three-dimensional model of a sample including one or more instances of a structure to be analyzed by the metrology tool; generate one or more predicted metrology images corresponding to a predicted analysis of the sample with the metrology tool based on the three-dimensional model, wherein the predicted metrology image includes predicted deviations from a two-dimensional projection of the three-dimensional model based on the predicted analysis of the sample with the metrology tool; evaluate two or more candidate metrology recipes for extracting a metrology measurement from the one or more predicted metrology images; select, based on one or more selection metrics, a metrology recipe from the two or more candidate metrology recipes for extracting a metrology measurement from an image of the structure from the metrology tool; receive, from the metrology tool, an output metrology image of a fabricated structure based on a metrology measurement of the fabricated structure; and extract the metrology measurement associated with the fabricated structure from the output metrology image based on the metrology recipe.