Molecular mechanics calculations of isobutene, its dimer (2,4,4-trimethyl-2-pentene), its trimer (2,4,4,6,6-pentamethyl-2-heptene), and seven families of coke molecules formed during n-butene isomerization were carried out within the ferrierite pore system. Monte Carlo docking showed that most of these molecules are well solvated by the zeolite framework and are preferentially sited within one or two intersections along the 10-membered ring channel. The locations of most of the larger coke molecules in two adjacent intersections account for the significant influence of dehydrogenative coupling in the formation of coke molecules in FER-structured zeolites. The stability of the butene dimer is close to that of molecules of carbonaceous compounds, which are known to be trapped inside the zeolite pores, whereas the stability of a trimer intermediate is much lower. This is consistent with the bimolecular isomerization mechanism and autocatalytic process proposed previously. Of the coke molecules investigated, only,fluoranthene is unstable in the FER pores. This suggests that fluoranthene is not completely located in the zeolite pores, and it is proposed that this molecule is formed at the pore mouth. The results of simulated diffusion calculations confirmed the minimum energy locations of biphenyl and naphthalene found by docking and were consistent with experimental data regarding the mobility of these two species in ferrierite.