A novel method called Impact-synchronous modal analysis (ISMA) was proposed previously which allows modal testing to be performed during operation. This technique focuses on signal processing of the upstream data to provide cleaner Frequency response function (FRF) estimation prior to modal extraction. Two important parameters, i.e., windowing function and impact force level were identified and their effect on the effectiveness of this technique were experimentally investigated. When performing modal testing during running condition, the cyclic loads signals are dominant in the measured response for the entire time history. Exponential window is effectively in minimizing leakage and attenuating signals of non-synchronous running speed, its harmonics and noises to zero at the end of each time record window block. Besides, with the information of the calculated cyclic force, suitable amount of impact force to be applied on the system could be decided prior to performing ISMA. Maximum allowable impact force could be determined from nonlinearity test using coherence function. By applying higher impact forces than the cyclic loads along with an ideal decay rate in ISMA, harmonic reduction is significantly achieved in FRF estimation. Subsequently, the dynamic characteristics of the system are successfully extracted from a cleaner FRF and the results obtained are comparable with Experimental modal analysis (EMA).