Display omitted •Innovative laser technique for THz spectroscopy.•Measurement of absorption and index of refraction in thin layer.•Numerical methods for data analysis.•Investigation of bilayer sample with micrometric thickness. THz time domain spectroscopy is a powerful technique enabling the investigation of different materials in the far-infrared frequency range. Even if nowadays this technique is well established, its application to very thin films remains particularly difficult. We investigated the utilization of THz spectroscopy on samples of micrometric thickness with the aim to disentangle multiple reflections and to measure with high accuracy the absolute values of the material parameters. We implemented an experimental and data analysis procedure that can be applied to free-standing single-layers or multi-layers samples. Specifically, we report on the experimental investigation by THz time domain spectroscopy of two samples: a test sample made of two layers of known thickness and materials; and a second sample, that is of a great interest for cultural heritage studies, made of a thin film of ink layered on a thicker support. Moreover, we describe in details the data analysis and fitting procedures needed to extract the material parameters from the experimental results.