As it is well-known, THz TDS is a modern tool for the detection and identification of substance. Often, in real conditions a substance under identification is covered by various materials (paper sheet, napkins, rag, and et.al). Therefore, the identification occurs for a substance covered by disordered structure, which acts for THz radiation as disordered photonic structure. In standard THz TDS method the substance detection carries out using a comparison of spectrum of a substance under consideration with spectra of the substances from database. Thus, an investigation of spectral medium response covered by disordered structure is very important for security and screening problem. Moreover, what we will see if we analyze a response from disordered structure without any dangerous substance? This question is a key one for practical application. Using computer simulation, we investigate below a propagation of laser pulse with a few cycles in a linear layered structure with random fluctuation of either layer dielectric permittivity or layers thicknesses or both characteristics of this structure. The process under consideration is described by 1D Maxwell’s equations. We show that a spectrum of pulse either reflected from substance or transmitted through substance depends in strong way from a number of random realization and fluctuating parameters of layered structure and an observer can see various absorption frequencies corresponding to dangerous substances. Nevertheless, we discuss one of possible ways for overcoming the influence of disordered structure on the observed spectrum.