This paper describes a head positioning controller in HDDs based on a dynamic characteristic of rolling friction. In the control system in HDDs, the head assembly was influenced the effect of several disturbances, e.g., RRO, flutter vibration, force disturbance, and so on. At the force disturbance, it caused by wind force, external shock, tension force of Flexible Printed Circuit, and rolling friction around pivot bearing. In these force disturbances, the influence of the rolling friction is large at positioning in minute area. Therefore, controlling the rolling friction is important at short span seeking for the high performance trajectory. In the past research, we proposed the friction model that considered about the dynamic characteristics of rolling friction. However, this model expressed only the friction motion of short span seeking operation, and was not able to express the friction characteristic of various operations. Therefore, we present a new friction model that considered a velocity characteristic based on Koizumi's model. And we propose a 2 DOF control system to suppress the effect of the rolling friction with dynamic characteristic. The effects of the proposed friction model and controller performance are verified by experimental results of short span seeking operation.