Thermophysical properties of materials and the optimization of the heat transfer are becoming more and more important for industrial applications of micro- and nanoelectronic devices. Thin layers in the micrometer to nanometer range are used to give specific functions to the devices. Since the thermophysical properties of thin layers differ from bulk material, this data is required for precise predictions of thermal management. One way to obtain the thermal properties of thin layers is the optical-based Time Domain Thermoreflectance (TDTR) method. To carry out TDTR measurements with a low level of uncertainty, the samples under study must meet requirements related to the surface roughness and a low level of optical scattering. The range of samples analysable by TDTR can be extended by applying the so-called bidirectional heat flow approach. This approach opens the possibility to assess thermal properties of materials with rough surfaces as well. The validity of the implemented model was shown by the characterisation of a test sample with well-known thermal properties fabricated for this purpose out of poly(methyl methacrylate) (PMMA) roughened with acetone:ethanol. The results obtained by TDTR measurements were compared to literature values, demonstrating the applicability of the bidirectional heat flow approach for this setup.