The present invention generally relates to the monitoring and controlling of a semiconductor manufacturing environment and, more particularly, to methods and systems for virtual meteorology (VM) applications based on data from multiple tools having heterogeneous relatedness. The methods and systems leverage the natural relationship of the multiple tools and take advantage of the relationship embedded in process variables to improve the prediction performance of the VM predictive wafer quality modeling. The prediction results of the methods and systems can be used as a substitute for or in conjunction with actual metrology samples in order to monitor and control a semiconductor manufacturing environment, and thus reduce delays and costs associated with obtaining actual physical measurements.