The semiconductor advanced packaging factory of the future must be fully digitalized to be agile and reconfigurable to support simultaneous high volume and high mix of products. To remain profitable, packaging facilities will need to support variable configurations, quantities, and industry applications, serving multiple customers. Unlike silicon wafer processing, semiconductor packaging encompasses myriad form factors, with the rise of heterogeneous integration through chiplets and System-in-Package technologies. Current packaging facilities follow a linear process flow, which leads to inefficiencies when managing product mixes. Tools often remain idle while waiting for upstream processes, resulting in suboptimal throughput. Although factory optimization is possible for a fixed product, switching factory setup between products is currently time consuming. Virtual twins of the chiplets, packages and equipment, linked to the PLM and MES systems, provide an agile mechanism to simulate reconfiguration of equipment and support on-demand virtual commissioning of new process and assembly flows.