Procedures for generating the standard Drosophila brain model with coordinate information are presented. A deterministic reference template is pursued for data integration and comparison. We propose a shape-averaging algorithm for creating the standard template, including axial and non-axial structures. The standard Drosophila brain comprises the standard cortex and the standard neuropils. The standard neuropils are located within the standard cortex with the average position and orientation. A global coordinate system for the brain cortex and local coordinate systems for the standard neuropils are also generated for the standard Drosophila brain. By placing each circuit into the standard brain, we can acquire the information about the spatial and temporal relationship among neurons.