This study deals with estimation of milling shape accuracy and trajectory conformity for small CNC 3D milling machines, based on vibration monitoring during the regular working cycles. The author made a large number of experimental tests, acquiring the acceleration signals, both on the milling tool-holder and on the bed frame. In order to evaluate the appropriate spectral characteristics of different machine parts and their weights on equipment dynamics, it was analyzed both the complete and the partial working cycle (such as forward tool motion, with or without effective milling, with or without tool driving, exclusively the milling cutter transitory/stabilized regime) for different basic milling shapes. The acceleration signals were jointly time-frequency investigated in order to evaluate specific spectral indicators related to the real motion characteristic of milling tool. It was used short time fast Fourier transform (STFFT) and Hough transform (HT) algorithms, along with stochastic evaluation of signal parameters, within time and frequency domains. The results reveal an accurate correlation between the specific transitory dynamics of the machine and the imposed milling shape. Main implications of the results within this analysis involve the noninvasive and facile investigation for milling errors of the CNC machine, conformity of tool head trajectory, identification of potential failure source, or damaged machine part.