Nanoscale antidot arrays were fabricated on a single-crystal microflake of topological insulator Bi2Te3. The introduction of antidot arrays significantly increased the resistance of the microflake, yet the temperature dependence of the resistance remains metallic. We observed that small oscillations that are periodic in magnetic field B appeared on top of the weak anti-localization magnetoresistance. Since the electron coherence length at low temperature becomes comparable to the feature size in our device, we argued that the magnetoresistance oscillations are the manifestation of quantum interference induced by the nanostructure. Our work demonstrates that the transport of topological insulators could indeed be controlled by artificially created nanostructures, and paves the way for future technological applications of this class of materials.