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The model used to represent musical instrument sounds plays a crucial role in the quality of sound transformations. Ideally, the representation should be compact and accurate, while its parameters should give flexibility to independently manipulate perceptually related features of the sounds. This work describes a source-filter model for musical instrument sounds based on the sinusoidal plus residual decomposition. The sinusoidal component is modeled as sinusoidal partial tracks (source) and a time-varying spectral envelope (filter), and the residual is represented as white noise (source) shaped by a time-varying spectral envelope (filter). This article presents estimation and representation techniques that give totally independent and intuitive control of the spectral envelope model and the frequencies of the partials to perform perceptually related sound transformations. The result of a listening test confirmed that, in general, the sounds resynthesized from the source-filter model are perceptually similar to the original recordings.