Blends of polymer and C60-derived molecules are in the spotlight in recent years for application in organic photovoltaics, forming what is known as bulk-heterojunction active layers. The character of the heterojunction is determinant, with clear relevance of morphology and phase separation. To better understand the morphology of the systems, we present a classical molecular dynamics (CMD) simulation of polymer/fullerene (P3HT/C60) blends, coming from different starting points, using the specifically designed Nanomol Force Field based on the Universal Force Field. We use not-so-short regioregular polymers with 30 hexyl-thiophene units (∼5kg⋅mol−1 molecular weight) and, adopting a ∼ 1:1 mass proportion for the polymer:molecule blend, we simulate cells of ∼ 40 thousand atoms, at room temperature and normal pressure conditions. We find that, independently of the starting-point spatial distribution of C60 molecules relative to P3HT chains, segregated or isotropic, the fullerene molecules show a tendency to segregate, and phase separation is the dominating regime.