Non-contact thickness measuring systems can be found in a wide spectrum of technologies. In this paper, Hilbert-Huang transform method is used to analyze the real time signals of a measuring system which includes two round conveyor strings carrying a thin plate, a solar wafer as a sample under test. The vibrations of moving strings and the plate, which are sensitive to moving speed and initial tension in the string, are introduced briefly; the relevant analyses should be helpful for the system design. Using EMD-based time-domain filtering and complementary method, thickness variations and error bands are estimated for different cases. The results show that HHT method as an adaptive time-frequency method, should be potential in measurement engineering applications.