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Sources of single photons are of fundamental importance in many applications as to provide quantum states for quantum communication and quantum information processing. Color centers in diamond are prominent candidates to generate and manipulate quantum states of light, even at room temperature. However, the efficiency of photon collection of the color centers in bulk diamond is greatly reduced by refraction at the diamond/air interface. To address this issue, diamond structuring has been investigated by various methods. Among them, focused-ion-beam (FIB) direct patterning has been recognized as the most favorable technique. But it has been noted that diamond tends to present significant challenges in FIB milling, e.g., the susceptibility of forming charging related artifacts and topographical features. In this work, periodically-positioned-rings and overlay patterning with stagger-superimposed-rings were proposed to alleviate some problems encountered in FIB milling of diamond, for improved surface morphology and shape control. Cross-scale network and uniform nanostructure arrays have been achieved in single crystalline diamond substrates. High quality diamond solid immersion lens and nanopillars were sculptured with a nitrogen-vacancy center buried at the desired position. Compared with the film counterpart, an enhancement of about ten folds in single photon collection efficiency was achieved with greatly improved signal to noise ratio. All these results indicate that FIB milling through over-lay patterning could be an effective approach to fabricate diamond structures, potentially for quantum information studies.