Molecular communication is a nanoscale communication method in which information is encoded in molecules. Molecular communication using microtubules in free space is one of the realistic scenarios proposed for this type of nanocommunication. Based on this technique, molecular communication via filaments using nano-relays is proposed in this paper to improve the performance of the system in terms of delay and bit error probability. An analytical model using jump diffusion processes is proposed for molecular propagation in this scenario. It is shown that the proposed mathematical model is capable of tracking molecular propagation in molecular communication via filaments using nano-relays. Also, the model is used to investigate effects of different parameters on delay and bit error probability.