Research institutions and industrial enterprises demand high accuracy and precision positioning systems to fulfil cutting edge requirements of up-to-date technological processes in the field of metrology and optical fabrication. Linear motor system design with high performance mechanical guiding system and optical encoder ensures nanometer scale precision and constant static error, which can be calibrated by optical instruments. Mechanical guiding systems has its benefits in case of control theory and its stability; unfortunately, on the other hand, there exists high influence of structure geometry and tribological effects such as friction and modal response. The aforementioned effect cannot be straightforwardly identified during the assembly process. Degradation of dynamic units can be detected only after certain operating time. Single degree of freedom systems are well investigated and the effect of degradation can be predicted, but there exists a gap in the analysis of nanometer scale multi degree of freedom dynamic systems; therefore, novel diagnostic tools need to be proposed. In this particular paper, dual axes dynamic system analysis will be presented. The main idea is to decouple standard stacked XY stage and analyse X and Y configuration as two different configurations of the same object, while imitators of corresponding axes are absolutely solid and stationary. As storage and analysis of time domain data is not efficient, main attention will be concentrated on frequency domain data, while, of course, statistical and graphical representation of dynamic response will be presented. Transfer function, dynamic response, spectral analysis of dynamic response, and modal analysis will be presented and discussed. Based on the collected data and its analysis, comparison of X and Y responses to different velocity excitation will be presented. Finally, conclusions and recommendations of novel diagnostic way will be presented.