The three omega method has proven to provide accurate and reliable measurements of thermal conductivity of thin films and other materials. However, if the films are soft and conductive, conventional methodologies to prepare samples for the measurement technique are challenging and often unachievable. Various modifications to the sample preparation to employ this technique for soft conducting films are reported in this paper including the use of shadow masks for metal heater deposition and a process for preparation of low temperature insulating films required between film and heater. In this work, thick (∼5μm) and ultrathin (∼110nm) films of polyaniline as well as a thin (∼300nm) film of low temperature plasma enhanced chemical vapor deposited SiO2 as a function of temperature were measured. Though not considered a soft material, the silicon dioxide film was utilized for comparison with previous data. Results indicate that the SiO2 film exhibits a thermal conductivity slightly lower than others’ data [S. M. Lee and D. G. Cahill, J. Appl. Phys. 81, 2590 (1997); H. Yan et al., Chem. Lett. 2000, 392; H. Yan et al., Anal. Calorim. 69, 881 (2002); J. E. de Albuquerque et al., Rev. Sci. Instrum. 74, 306 (2003)], which is likely due to the low temperature processing conditions that results in additional disorder in the film. The polyaniline films exhibit an increase in thermal conductivity with temperature, which is largely due to increasing heat capacity. The thick film thermal conductivity is many times the value corresponding to the thin film, which is likely due to significant phonon boundary scattering present in the ultrathin film.