The spatial polarisation distribution in inhomogeneously polar molecular crystals has been imaged by scanning pyroelectric tomography and simulated by a Markov process. The experimental technique combines scanning pyroelectric microscopy (SPEM) with layerwise thinning of crystals. The SPEM probes the local spontaneous polarisation by its temperature dependence (pyroelectric effect). A focused and intensity modulated laser beam scans the surface of a polar sample and induces temperature changes in a volume depending on the laser spot size and the thermal diffusion length lambda(th) Since high lateral resolution of the SPEM is only available for small values of lambda(th) depth information to a resolution of similar to 10 mu m is achieved by repeated scanning and stepwise thinning of crystals. A layer by layer technique can provide 3D imaging of the polar ordering with a lateral resolution of similar to 20 mu m at a probed layer thickness of similar to 10 mu m. Applied to perhydrotriphenylene (PI-ITP) co-crystallised with 1-(4-nitrophenyl)piperazine (NPP) two conical macro-domains of opposite and nearly constant polarisation were found. The SPEM results are in good agreement with a homogeneous Markov chain model driving dipolar molecules into a parallel state within channels of PHTP. The new tomographic view reveals that the opposing cones are partially overlapping at the tips. Lateral growth processes are assumed to be responsible for this. A theoretical section covers aspects of the convergency into the polar state and the length of polar chains discussed in terms of intermolecular interaction energies.