Many mechanical systems contains flexible joints. The main problem in control of these kinds of objects are oscillations. The control strategy can be supplied by signal shaping methods. One of the simplest and most effective algorithm of reference signal shaping is named input shaping. The problem of input shaping tuning can be automatized. The paper shows two basic algorithms of input shaping autotuning. Every tuning method needs the information of object’s natural oscillation frequencies and their damping. These information are extracted using object identification and Fast Fourier Transform. Algorithms were tested by simulation on simple objects and on a model of two-mass system. The research was made in Matlab/Simulink environment.