The finite length of a Taylor-Couette cell introduces endwall effects that interact with the centrifugal instability. We investigate the interaction between the endwall Ekman boundary layers and the vortical structures in a finite-length cavity with counter-rotating cylinders via direct numerical simulation using a three-dimensional spectral method. To analyze the nature of the interaction between the vortices and the endwall layers we consider four endwall boundary conditions: fixed endwalls, endwalls rotating with the outer cylinder, endwalls rotating with the inner cylinder, and stress-free endwalls. The vortical structure of the flow depends on the endwall conditions. The waviness of the vortices is suppressed only very near the endwall, primarily due to zero axial velocity at the endwall rather than viscous effects. In spite of their waviness and random behavior, the vortices generally stay inside of the vθ=0 isosurface by adjusting quickly to the radial transport of azimuthal momentum. The thickness and strength of the Ekman layer at the endwall match with that predicted from a simple theoretical approach.