The [CII] 158um emission line can arise in all phases of the ISM, therefore being able to disentangle its relative contribution is an important, yet unresolved, problem when undertaking galaxy wide observations. We present a new multi-phase 3D radiative transfer code, through the coupling of Starburst99 with MOCASSIN and 3D-PDR, and model 3D star forming regions in an attempt to simulate the total gas content of galaxies across all phases of the ISM. By investigating parameter space, and applying a Bayesian Inference methodology and a Random Forest Machine Learning technique, we parametrise how the relative fraction of [CII] emission from molecular regions varies as a function of physical properties of galaxies; we hereby report this novel prescription which observers can use when undertaking galaxy-wide [CII] observations. We find the main parameters responsible are specific star formation rate (sSFR), which controls the size of the HII regions, gas phase metallicity and HII region electron number density, that both control the equilibrium conditions and cooling rates, and finally dust mass fraction, which controls the total size of the ionised, neutral and molecular regions. Overall we find that an increase in the HII region electron number density leads to an increase in the fraction of [CII] emission originating from molecular regions, while a decrease in sSFR leads to a similar increase. We then apply our new prescription to the Herschel Reference Survey sample of galaxies and find that approximately 60-80% of the total integrated [CII] emission, on galaxy wide scales, in the local universe, will arise from molecular regions. This work will help aid our understanding on the physical environments where [CII] emission can be used as an accurate star formation rate tracer, while constraining the fraction of CO-dark gas in the local universe.