This paper describes a development of a loop filter design in a physical modeling of the plucked string instrument. The conventional method proposed by V$"{a}$lim$"{a}$ki cannot estimate right parameters if a sound has either very short sustain or no sustain. In order to overcome this drawback, we propose the use of the decay region and 5 to 20 harmonics of the sound in the estimation of loop filter parameters. The most appropriate filter coefficient is chosen by frequency signal to noise ratio. To verify the performance of the proposed method, the guitar, gayageum and geomungo were selected as the target because they have different shape, structure, and material of strings. Regardless of the duration of harmonics, the proposed method was able to estimate the loop filter parameters representing frequency-dependent damping of harmonics.