Recently, a decelerator for neutral polar molecules has been presented that operates on the basis of macroscopic, three-dimensional, traveling electrostatic traps [A. Osterwalder, S. A. Meek, G. Hammer, H. Haak, and G. Meijer, Phys. Rev. A 81, 051401 (2010)]10.1103/PhysRevA.81.051401. In the present paper, a complete description of this decelerator is given, with emphasis on the electronics and the mechanical design. Experimental results showing the transverse velocity distributions of guided molecules are shown and compared to trajectory simulations. An assessment of non-adiabatic losses is made by comparing the deceleration signals from 13CO with those from 12CO and with simulated signals.