Three-dimensional topological insulators are a new kind of quantum matter featured with gapless Dirac-like energy-dispersive surface states in the insulating bulk band gaps. However, in experiment, it is difficult to study quantum interference effect of surface states due to considerable contribution from bulk carriers in thick bulk material. To suppress such a bulk state contribution, nanostructures, such as ultra-thin films, nanowires and nanoribbons, have been employed in the study of quantum interference effects of the surface states. Here, we report on a magnetotransport measurement study of nanoscaled antidot array devices made from three-dimensional topological insulator Bi2Se3 thin films. The antidot arrays with hundreds of nanometers in diameter and edge-to-edge distance are fabricated in the thin films by utilizing the focused-ion beam technique, and the magnetotransport properties of the fabricated devices are measured at low temperatures. The results of the magnetotransport measurements for three representative devices, denoted as Dev-1 (with no antidot array fabricated), Dev-2 (with an antidot array of a relatively large period), and Dev-3 (with an antidot array of a relatively small period), are reported in this work. Weak anti-localization indicated by a sharp peak of conductivity at zero magnetic field is observed in all the three devices. Through theoretical fitting to the measurement data, the transport parameters in the three devices, such as spin-orbit coupling length Lso, phase coherence length L, and the number of conduction channels , are extracted. The extracted Lso value is tens of nanometers, which is consistent with the presence of the strong spin-orbit interaction in the Bi2Se3 thin film. The extracted L value is hundreds of nanometers and increases exponentially with temperature decreasing. It is found that the magnetotransports in Dev-1 and Dev-2 are well characterized by the coherent transport through a single conduction channel. For Dev-3, the magnetotransport at low temperatures is described by the coherent transport through two independent conduction channels, while at elevated temperatures the magnetotransport is dominantly described by the transport through one single conduction channel. Unlike the case where the transport occurs dominantly through a single conduction channel, the transport through two independent conduction channels in Dev-3 implies that at least one surface channel is present in the device.