The complexity of drilling carbon fiber reinforced polymers (CFRP) requires accurate predictive models. This study addresses the challenge using an ensemble machine learning (ML) approach with stacked generalization. The model captures the relationships between key input variables—such as graphene nanoplatelet (GNP) content, ultrasonic assistance, tool type, stacking sequence, and feed rate—and output parameters, specifically thrust force and delamination. A nested feature scoring (NFS) method was employed for importance analysis, revealing tooling type and feed rate as key features for minimizing delamination and reducing thrust force, respectively. The machinability results revealed that ultrasonic drilling lowered thrust force by improving chip evacuation and reducing fiber breakage. HSS tools with cobalt content, alongside symmetrical stacking sequence, helped to further minimize both thrust force and delamination. However, the inclusion of GNPs led to an increase in thrust force and delamination, attributed to the increased strength of the CFRP/GNP composite. The process involved meticulous training, resulting in four optimal-fit models serving as inputs for the stacked meta-model. Iterative enhancements fortified the ensemble robustness, with fine-tuning of hyperparameters through Bayesian optimization. The ensemble superiority over individual models manifested in a remarkable reduction of mean absolute error (MAE) and root mean squared error (RMSE) by up to 97% and 124% for delamination, and 205% and 154% for thrust force, compared to the best base learner. Visual and statistical assessments effectively illuminated the intricate interactions between variables in the drilling process. The methodology resulted in a highly adaptable predictive model with applications across diverse manufacturing contexts.@en