Heat transport at the microscale is of vital importace in microtechnology applications. The heat transport equation is different from the traditional heat transport equation since a second order derivative of temperature with respect to time and a third-order mixed derivative of temperature with respect to space and time are introduced. In this study, we develop a hybrid finite element-finite difference (FE-FD) scheme with two levels in time for the three dimensional heat transport equation in a cylindrical thin film with sub-microscale thickness. It is shown that the scheme is unconditionally stable. The scheme is then employed to obtain the temperature rise in a sub-microscale cylindrical gold film. The method can be applied to obtain the temperature rise in any thin films with sub-microscale thickness, where the geometry in the planar direction is arbitrary.