Over the past few years, the virtual metrology (VM) technology has been proposed and developed and several VM related papers have been published. These proposed VM architectures are mainly applied for conjecturing single-stage or direct processing quality. However, the processing quality of some of manufacturing processes cannot be measured directly. Those single-stage VM architectures may not be applied to handle this indirect VM problem accurately. To properly handle this indirect VM problem, the paper proposes a dual-stage indirect VM architecture (DIVMA), which involves two process tools, to handle the indirect VM problem. In Stage I, the direct VM model of the fore-tool is established as usual, and then the indirect VM model of the rear-tool is built in Stage II that involves the Stage-I VM output. The concept of virtual cassette is also proposed in the paper. The chemical vapor deposition (CVD) process of a fifth generation TFT-LCD fab in Chi Mei Optoelectronics Corporation (CMO), Taiwan is adopted to test and compare the conjecture accuracy without and with the virtual cassette and the proposed DIVMA. Experimental results demonstrate that the virtual-cassette concept is valid for improving VM conjecturing accuracy; also this DIVMA is adequate for handling the indirect VM problem that has a coupling effect between those two subsequent tools.