The sharpness of FBAR filters are determined by mechanical Q factors (Qm) of piezoelectric thin films when other electrical loss is negligibly small. In this study, we introduce a new method for estimating Qm of films using piezoelectric film/substrate structures (HBAR structures) without using self-standing film structures. When Qm of the film (Qpiezo) is lower than that of the substrate (Qsub), Q factor of the entire HBAR (QHBAR) decrease due to the dumping of the film which have larger mechanical loss, only in the vicinity of the resonant frequency. Therefore, Qpiezo can be estimated from the amount of reduction in the QHBAR when Qsub is known. We investigated whether the differences of the Qm factor among various samples are able to be detected. Obvious decrease of experimental QHBAR in the vicinity of the resonant frequency of each film was observed as expected. The amount of reduction of ScAlN is larger than that of pure AlN, indicating that mechanical Qpiezo of ScAlN is lower than that of pure AlN as expected.