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Nanomechanical resonators have a huge potential for a variety of applications, including high-resolution mass sensing. In this paper, we demonstrate a novel rapid prototyping method for fabricating nanoelectromechanical systems using focused-ion-beam milling as well as in situ electromechanical characterization using a transmission electron microscope. Nanomechanical resonators were cut out of thin membrane chips, which have been prefabricated using standard cleanroom processing. We have demonstrated the fabrication of double-clamped beams with feature sizes down to 200 nm using a fabrication time of 30 min per device. Afterwards, the dynamic and structural properties of a double-clamped beam were measured after subsequent Joule heating events in order to ascertain the dependence of the internal structure on the Q-factor and resonant frequency of the device. It was observed that a change from amorphous to polycrystalline silicon structure significantly increased the resonant frequency as well as the Q-factor of the nanomechanical resonator. Aside from allowing detailed studies of the correlation between internal structure and nanomechanical behavior on an individual rather than a statistical basis, the combination of a short turnaround time and in situ nonlithographic tuning of the properties provide a flexible approach to the development and prototyping of nanomechanical devices.