The relative stability of possible arrangements of the pterocarpan fused ring system and the conformational preferences of the side chains present in two natural compounds, 3,9-dimethoxy-4-prenylpterocarpan (bitucarpin A) and 3,9-dihydroxy-4,8-diprenylpterocarpan (erybraedin C), have been investigated in vacuo on a number of stereoisomers (either natural or not) at the B3LYP/6-31G* level. The results obtained using three classical force fields (Tripos/GH, MMFF94 and GAFF), compared to the quantum mechanical ones for selected torsions (hydroxyl and prenyl group rotations), indicate that MMFF94 produces a satisfactory description of structural features of pterocarpans, and thus it is advisable to resort to it when thorough ab initio or DFT investigations are not affordable. Two stable structures, named Ht and Ot from the substituent at the tetrahedral carbon vicinal to the chiral centre in trans position with respect to its H, have been found for the cis fused ring system, with Ht about 2 kcal mol−1 more favourable than Ot. The interconversion between Ht and Ot can occur along two pathways with distinct values of the dihedral angle between the benzofuran O and the peri C of chromane. For both stable skeleton arrangements there are a number of almost equivalent minima separated by considerably high barriers, in 3,9-dihydroxypterocarpan for the OH group rotations, and in bitucarpin A or in erybraedin C for the prenyl side chain rotations. For trans configurations, which are about 10 kcal mol−1 less favourable than cis configurations, only Ht arrangements have been located. In the case of erybraedin C, the structures obtainable by coupling on the two side chains in all possible ways the prenyl dihedral values related to minima in bitucarpin A have been studied with a single orientation of each hydroxy group. Starting from that hydroxy group arrangement, MMFF94 PES have been examined either for each minimum in the conserved prenyl chain or for changes in the second dihedrals while the first ones have been kept in the region of their minimum (both prenyl side chains almost perpendicular to the pterocarpan scaffold).