This paper presents a pre-shaking technique for measuring the Vs profile of sand deposits and determining the natural frequencies of the sand bed and soil-structure system in a centrifuge model at an acceleration of 80 g. The pre-shaking technique is a non-destructive test. It uses a shaker as a wave generation source and a vertical array of accelerometers embedded in the sand bed and the accelerometers attached to the pile head as receivers. The pre-shaking method can be easily used for in-flight subsurface exploration (Vs profile measurements) and in-flight system identification of soil-structure systems (natural frequency measurements). A soil-pile centrifuge model is used to demonstrate the versatility of pre-shaking during a routine centrifuge shaking table test. This paper discusses the testing setup, testing procedures, related SI techniques, and signal processing for the soil-pile system. The natural frequencies measured by the pre-shaking tests are consistent with theory-based results. This technique can be conducted at any time before and after major earthquake events occur in a test.