We discuss Bohmian paths of the two-level atoms moving in a waveguide through an external resonance-producing field, perpendicular to the waveguide, and localized in a region of finite diameter. The time spent by a particle in a potential region is not well-defined in the standard quantum mechanics, but it is well-defined in the Bohmian mechanics. Bohms theory is used for calculating the average time spent by a transmitted particle inside the field region and the arrival-time distributions at the edges of the field region. Using the Runge-Kutta method for the integration of the guidance law, some Bohmian trajectories were also calculated. Numerical results are presented for the special case of a Gaussian wave packet.